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
RLF	6018	broad.mit.edu	36	1	40399896	40399896	+	Splice_Site_SNP	SNP	G	G	T	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Splice_Site_SNP	SNP	40399896	40399896	RLF	1	G	G	T	44
LEFTY1	10637	broad.mit.edu	36	1	224141128	224141128	+	Silent	SNP	G	G	T	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	224141128	224141128	LEFTY1	1	G	G	T	45
SVIL	6840	broad.mit.edu	36	10	29816115	29816115	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	29816115	29816115	SVIL	10	C	C	T	19
RGR	5995	broad.mit.edu	36	10	85998718	85998718	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	85998718	85998718	RGR	10	G	G	A	40
OR5L2	26338	broad.mit.edu	36	11	55351473	55351473	+	Missense_Mutation	SNP	T	T	C	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	55351473	55351473	OR5L2	11	T	T	C	64
ATL3	25923	broad.mit.edu	36	11	63183284	63183284	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	63183284	63183284	ATL3	11	G	G	A	46
RASGRP2	10235	broad.mit.edu	36	11	64264122	64264123	+	Missense_Mutation	DNP	TC	TC	GA	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	DNP	64264122	64264123	RASGRP2	11	TC	TC	GA	54
LRRK2	120892	broad.mit.edu	36	12	38994218	38994218	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	38994218	38994218	LRRK2	12	G	G	A	38
KRT85	3891	broad.mit.edu	36	12	51047140	51047140	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	51047140	51047140	KRT85	12	G	G	A	40
UTP20	27340	broad.mit.edu	36	12	100281580	100281580	+	Nonsense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Nonsense_Mutation	SNP	100281580	100281580	UTP20	12	C	C	G	19
CCDC64	92558	broad.mit.edu	36	12	119015307	119015307	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	119015307	119015307	CCDC64	12	G	G	A	38
FOXG1	2290	broad.mit.edu	36	14	28306971	28306971	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	28306971	28306971	FOXG1	14	C	C	T	20
MLH3	27030	broad.mit.edu	36	14	74585341	74585341	+	Silent	SNP	T	T	C	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	74585341	74585341	MLH3	14	T	T	C	58
MAP1A	4130	broad.mit.edu	36	15	41605892	41605892	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	41605892	41605892	MAP1A	15	G	G	A	42
BFAR	51283	broad.mit.edu	36	16	14651187	14651187	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	14651187	14651187	BFAR	16	G	G	A	34
NUDT7	283927	broad.mit.edu	36	16	76316983	76316983	+	Splice_Site_SNP	SNP	G	G	T	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Splice_Site_SNP	SNP	76316983	76316983	NUDT7	16	G	G	T	44
TP53	7157	broad.mit.edu	36	17	7519168	7519168	+	Missense_Mutation	SNP	A	A	G	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	7519168	7519168	TP53	17	A	A	G	15
NF1	4763	broad.mit.edu	36	17	26573001	26573001	+	Missense_Mutation	SNP	T	T	C	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	26573001	26573001	NF1	17	T	T	C	55
EZH1	2145	broad.mit.edu	36	17	38125994	38125995	+	Splice_Site_SNP	DNP	CT	CT	AC	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Splice_Site_SNP	DNP	38125994	38125995	EZH1	17	CT	CT	AC	32
DUS1L	64118	broad.mit.edu	36	17	77614135	77614135	+	Missense_Mutation	SNP	A	A	G	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	77614135	77614135	DUS1L	17	A	A	G	5
RBBP8	5932	broad.mit.edu	36	18	18856129	18856129	+	Silent	SNP	T	T	C	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	18856129	18856129	RBBP8	18	T	T	C	52
ZNF236	7776	broad.mit.edu	36	18	72788516	72788516	+	Nonsense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Nonsense_Mutation	SNP	72788516	72788516	ZNF236	18	G	G	T	47
KISS1R	84634	broad.mit.edu	36	19	871425	871425	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	871425	871425	KISS1R	19	G	G	C	43
ZNF181	339318	broad.mit.edu	36	19	39923763	39923763	+	Missense_Mutation	SNP	A	A	G	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	39923763	39923763	ZNF181	19	A	A	G	13
PPP2R1A	5518	broad.mit.edu	36	19	57406487	57406487	+	Missense_Mutation	SNP	A	A	C	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	57406487	57406487	PPP2R1A	19	A	A	C	6
KCNS3	3790	broad.mit.edu	36	2	17976889	17976889	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	17976889	17976889	KCNS3	2	C	C	T	23
GTF3C2	2976	broad.mit.edu	36	2	27405843	27405843	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	27405843	27405843	GTF3C2	2	C	C	T	23
KCNK12	56660	broad.mit.edu	36	2	47602342	47602342	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	47602342	47602342	KCNK12	2	G	G	A	46
WIPF1	7456	broad.mit.edu	36	2	175145134	175145134	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	175145134	175145134	WIPF1	2	G	G	A	39
FZD5	7855	broad.mit.edu	36	2	208340499	208340499	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	208340499	208340499	FZD5	2	C	C	A	19
ABCB6	10058	broad.mit.edu	36	2	219791287	219791287	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	219791287	219791287	ABCB6	2	C	C	G	26
LRRFIP1	9208	broad.mit.edu	36	2	238336867	238336867	+	Missense_Mutation	SNP	T	T	C	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	238336867	238336867	LRRFIP1	2	T	T	C	60
MOV10L1	54456	broad.mit.edu	36	22	48888779	48888779	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	48888779	48888779	MOV10L1	22	C	C	G	21
FAM19A1	407738	broad.mit.edu	36	3	68549253	68549253	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	68549253	68549253	FAM19A1	3	C	C	T	27
SCHIP1	29970	broad.mit.edu	36	3	161086767	161086767	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	161086767	161086767	SCHIP1	3	G	G	A	36
SI	6476	broad.mit.edu	36	3	166267839	166267839	+	Missense_Mutation	SNP	T	T	A	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	166267839	166267839	SI	3	T	T	A	64
PCDHAC2	56134	broad.mit.edu	36	5	140327822	140327822	+	Silent	SNP	A	A	G	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	140327822	140327822	PCDHAC2	5	A	A	G	11
CLINT1	9685	broad.mit.edu	36	5	157169305	157169305	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	157169305	157169305	CLINT1	5	C	C	T	24
HSPA1A	3303	broad.mit.edu	36	6	31893249	31893249	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	31893249	31893249	HSPA1A	6	G	G	A	40
TNXB	7148	broad.mit.edu	36	6	32137401	32137401	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	32137401	32137401	TNXB	6	C	C	G	22
PKD1L1	168507	broad.mit.edu	36	7	47817969	47817969	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	47817969	47817969	PKD1L1	7	C	C	T	28
PPP1R9A	55607	broad.mit.edu	36	7	94735879	94735879	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	94735879	94735879	PPP1R9A	7	G	G	C	33
MYOM2	9172	broad.mit.edu	36	8	2034099	2034099	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	2034099	2034099	MYOM2	8	C	C	T	19
DOCK5	80005	broad.mit.edu	36	8	25255872	25255872	+	Missense_Mutation	SNP	A	A	G	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	25255872	25255872	DOCK5	8	A	A	G	2
PRKDC	5591	broad.mit.edu	36	8	48968400	48968400	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	48968400	48968400	PRKDC	8	C	C	T	23
SDC2	6383	broad.mit.edu	36	8	97674951	97674951	+	Missense_Mutation	SNP	T	T	G	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	97674951	97674951	SDC2	8	T	T	G	59
SCRIB	23513	broad.mit.edu	36	8	144963074	144963074	+	Missense_Mutation	SNP	A	A	T	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	144963074	144963074	SCRIB	8	A	A	T	12
PTPRD	5789	broad.mit.edu	36	9	8321723	8321723	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	8321723	8321723	PTPRD	9	C	C	T	31
IFNA13	3447	broad.mit.edu	36	9	21357904	21357904	+	Missense_Mutation	SNP	T	T	A	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	21357904	21357904	IFNA13	9	T	T	A	55
TRPM3	80036	broad.mit.edu	36	9	72667692	72667692	+	Silent	SNP	A	A	C	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	72667692	72667692	TRPM3	9	A	A	C	3
OR13C5	138799	broad.mit.edu	36	9	106400815	106400815	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	106400815	106400815	OR13C5	9	C	C	A	32
ODF2	4957	broad.mit.edu	36	9	130273486	130273486	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	130273486	130273486	ODF2	9	C	C	G	21
NUP188	23511	broad.mit.edu	36	9	130782721	130782721	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	130782721	130782721	NUP188	9	C	C	G	24
ITGB1BP2	26548	broad.mit.edu	36	X	70439016	70439016	+	Missense_Mutation	SNP	A	A	G	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	70439016	70439016	ITGB1BP2	23	A	A	G	9
AFF2	2334	broad.mit.edu	36	X	147726897	147726897	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	147726897	147726897	AFF2	23	C	C	T	30
KIAA0430	9665	broad.mit.edu	36	16	15612940	15612959	+	Splice_Site_Del	DEL	ATCAACTCACCAGTGATAAG	-	ATCAACTCACCAGTGATAAG	novel	Unknown	TCGA-09-2053-01	TCGA-09-2053-10							Unknown	Unknown	Unknown	Phase_I	Capture	---			Illumina GAIIx	Broad	Splice_Site_Del	DEL	15612940	15612959	KIAA0430	16	ATCAACTCACCAGTGATAAG	-	ATCAACTCACCAGTGATAAG	8