Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	dataset	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context
ABCG1	9619	hgsc.bcm.edu	36	21	42581464	42581464	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	42581464	42581464	ABCG1	21	G	G	T	41
ACACB	32	hgsc.bcm.edu	36	12	108107791	108107791	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	108107791	108107791	ACACB	12	C	C	T	23
ARMCX2	9823	hgsc.bcm.edu	36	X	100798969	100798969	+	Missense_Mutation	SNP	A	A	C	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	100798969	100798969	ARMCX2	23	A	A	C	11
CACNG3	10368	hgsc.bcm.edu	36	16	24265617	24265617	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Silent	SNP	24265617	24265617	CACNG3	16	G	G	A	35
CASKIN2	57513	hgsc.bcm.edu	36	17	71013282	71013282	+	Missense_Mutation	SNP	T	T	G	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	71013282	71013282	CASKIN2	17	T	T	G	60
CES7	221223	hgsc.bcm.edu	36	16	54438072	54438072	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	54438072	54438072	CES7	16	G	G	A	33
CHML	1122	hgsc.bcm.edu	36	1	239863810	239863810	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	239863810	239863810	CHML	1	G	G	A	41
COL6A3	1293	hgsc.bcm.edu	36	2	237930743	237930743	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	237930743	237930743	COL6A3	2	C	C	T	24
CRP	1401	hgsc.bcm.edu	36	1	157950307	157950307	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	157950307	157950307	CRP	1	C	C	T	31
DCTN1	1639	hgsc.bcm.edu	36	2	74450063	74450063	+	Silent	SNP	G	G	T	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Silent	SNP	74450063	74450063	DCTN1	2	G	G	T	38
DDIT3	1649	hgsc.bcm.edu	36	12	56197026	56197026	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	56197026	56197026	DDIT3	12	C	C	T	26
DDR1	780	hgsc.bcm.edu	36	6	30964747	30964747	+	Missense_Mutation	SNP	A	A	G	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	30964747	30964747	DDR1	6	A	A	G	6
EIF3B	8662	hgsc.bcm.edu	36	7	2381578	2381578	+	Missense_Mutation	SNP	A	A	G	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	2381578	2381578	EIF3B	7	A	A	G	6
ERN2	10595	hgsc.bcm.edu	36	16	23611111	23611111	+	Missense_Mutation	SNP	A	A	T	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	23611111	23611111	ERN2	16	A	A	T	15
FABP4	2167	hgsc.bcm.edu	36	8	82553699	82553699	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	82553699	82553699	FABP4	8	C	C	T	19
FAM111A	63901	hgsc.bcm.edu	36	11	58677422	58677422	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	58677422	58677422	FAM111A	11	C	C	G	31
FAM47B	170062	hgsc.bcm.edu	36	X	34872017	34872017	+	Nonsense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Nonsense_Mutation	SNP	34872017	34872017	FAM47B	23	G	G	A	47
FASTKD3	79072	hgsc.bcm.edu	36	5	7920785	7920785	+	Missense_Mutation	SNP	A	A	C	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	7920785	7920785	FASTKD3	5	A	A	C	5
FBXO47	494188	hgsc.bcm.edu	36	17	34354744	34354744	+	Missense_Mutation	SNP	T	T	A	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	34354744	34354744	FBXO47	17	T	T	A	63
GPR112	139378	hgsc.bcm.edu	36	X	135218642	135218642	+	Missense_Mutation	SNP	A	A	C	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	135218642	135218642	GPR112	23	A	A	C	12
GRM8	2918	hgsc.bcm.edu	36	7	125960644	125960644	+	Missense_Mutation	SNP	T	T	C	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	125960644	125960644	GRM8	7	T	T	C	49
KANK1	23189	hgsc.bcm.edu	36	9	728303	728303	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	728303	728303	KANK1	9	C	C	A	24
MAN1A1	4121	hgsc.bcm.edu	36	6	119567731	119567731	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	119567731	119567731	MAN1A1	6	G	G	C	36
MTSS1	9788	hgsc.bcm.edu	36	8	125649854	125649854	+	Missense_Mutation	SNP	T	T	C	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	125649854	125649854	MTSS1	8	T	T	C	50
MYST4	23522	hgsc.bcm.edu	36	10	76451914	76451914	+	Silent	SNP	A	A	G	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Silent	SNP	76451914	76451914	MYST4	10	A	A	G	3
NBAS	51594	hgsc.bcm.edu	36	2	15276500	15276500	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	15276500	15276500	NBAS	2	G	G	A	42
NCKAP1	10787	hgsc.bcm.edu	36	2	183556332	183556332	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	183556332	183556332	NCKAP1	2	C	C	A	27
NR4A2	4929	hgsc.bcm.edu	36	2	156892706	156892706	+	Frame_Shift_Del	DEL	T	T	-	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Frame_Shift_Del	DEL	156892706	156892706	NR4A2	2	T	T	-	54
NRG1	3084	hgsc.bcm.edu	36	8	32625385	32625385	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	32625385	32625385	NRG1	8	C	C	A	26
PBRM1	55193	hgsc.bcm.edu	36	3	52660820	52660820	+	Missense_Mutation	SNP	T	T	C	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	52660820	52660820	PBRM1	3	T	T	C	56
PDE6C	5146	hgsc.bcm.edu	36	10	95390680	95390680	+	Missense_Mutation	SNP	A	A	C	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	95390680	95390680	PDE6C	10	A	A	C	3
SCN3A	6328	hgsc.bcm.edu	36	2	165655734	165655734	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Silent	SNP	165655734	165655734	SCN3A	2	G	G	A	36
SEC23A	10484	hgsc.bcm.edu	36	14	38584206	38584206	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	38584206	38584206	SEC23A	14	C	C	T	19
SEC61A1	29927	hgsc.bcm.edu	36	3	129268566	129268566	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	129268566	129268566	SEC61A1	3	C	C	T	19
TLL2	7093	hgsc.bcm.edu	36	10	98123358	98123358	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	98123358	98123358	TLL2	10	C	C	T	26
TNFAIP3	7128	hgsc.bcm.edu	36	6	138237686	138237686	+	Missense_Mutation	SNP	T	T	G	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	138237686	138237686	TNFAIP3	6	T	T	G	63
TOM1	10043	hgsc.bcm.edu	36	22	34047995	34047995	+	Missense_Mutation	SNP	A	A	C	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	34047995	34047995	TOM1	22	A	A	C	9
TP53	7157	hgsc.bcm.edu	36	17	7519015	7519015	+	Splice_Site_SNP	SNP	C	C	T	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Splice_Site_SNP	SNP	7519015	7519015	TP53	17	C	C	T	24
TRIM73	375593	hgsc.bcm.edu	36	7	74870941	74870941	+	Missense_Mutation	SNP	A	A	C	rs3095183	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	74870941	74870941	TRIM73	7	A	A	C	1
TSHZ2	128553	hgsc.bcm.edu	36	20	51306452	51306452	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Silent	SNP	51306452	51306452	TSHZ2	20	G	G	A	38
TSHZ3	57616	hgsc.bcm.edu	36	19	36462022	36462022	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	36462022	36462022	TSHZ3	19	C	C	T	26
WNT2	7472	hgsc.bcm.edu	36	7	116747964	116747964	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	116747964	116747964	WNT2	7	C	C	T	26
YIPF2	78992	hgsc.bcm.edu	36	19	10895080	10895080	+	Frame_Shift_Del	DEL	A	A	-	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Frame_Shift_Del	DEL	10895080	10895080	YIPF2	19	A	A	-	14
ZNF691	51058	hgsc.bcm.edu	36	1	43090048	43090048	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	43090048	43090048	ZNF691	1	C	C	G	17
ZNF804A	91752	hgsc.bcm.edu	36	2	185439358	185439358	+	Missense_Mutation	SNP	A	A	T	novel	Unknown	TCGA-09-1661-01	TCGA-09-1661-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_III	Capture	Unknown	.	.	SOLID	Baylor	Missense_Mutation	SNP	185439358	185439358	ZNF804A	2	A	A	T	1