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
PDPN	10630	broad.mit.edu	36	1	13809526	13809526	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	13809526	13809526	PDPN	1	G	G	C	33
FMO5	2330	broad.mit.edu	36	1	145139448	145139448	+	Missense_Mutation	SNP	T	T	G	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	145139448	145139448	FMO5	1	T	T	G	60
FCRL2	79368	broad.mit.edu	36	1	155985361	155985361	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	155985361	155985361	FCRL2	1	G	G	A	42
AKR1C1	1645	broad.mit.edu	36	10	4998131	4998131	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	4998131	4998131	AKR1C1	10	C	C	A	26
ZNF33A	7581	broad.mit.edu	36	10	38384567	38384567	+	Silent	SNP	G	G	C	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10			G	C	G	G	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Silent	SNP	38384567	38384567	ZNF33A	10	G	G	C	41
HSPA12A	259217	broad.mit.edu	36	10	118424738	118424738	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	118424738	118424738	HSPA12A	10	G	G	A	44
AHNAK	79026	broad.mit.edu	36	11	62055266	62055266	+	Missense_Mutation	SNP	T	T	C	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	62055266	62055266	AHNAK	11	T	T	C	50
KCNA1	3736	broad.mit.edu	36	12	4891810	4891810	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10			C	T	C	C	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Silent	SNP	4891810	4891810	KCNA1	12	C	C	T	31
MAPKAPK5	8550	broad.mit.edu	36	12	110802716	110802716	+	Splice_Site_SNP	SNP	T	T	A	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10			T	A	T	T	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Splice_Site_SNP	SNP	110802716	110802716	MAPKAPK5	12	T	T	A	57
SKA3	221150	broad.mit.edu	36	13	20648551	20648551	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	20648551	20648551	SKA3	13	C	C	T	23
POTEB	339010	broad.mit.edu	36	15	19336052	19336052	+	Silent	SNP	A	A	T	rs28566570	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	19336052	19336052	POTEB	15	A	A	T	7
HERC2	8924	broad.mit.edu	36	15	26132622	26132622	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10			C	T	C	C	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Missense_Mutation	SNP	26132622	26132622	HERC2	15	C	C	T	27
FHOD1	29109	broad.mit.edu	36	16	65838802	65838802	+	Nonsense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Nonsense_Mutation	SNP	65838802	65838802	FHOD1	16	C	C	A	30
PKD1L2	114780	broad.mit.edu	36	16	79745444	79745444	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	79745444	79745444	PKD1L2	16	C	C	A	18
TP53	7157	broad.mit.edu	36	17	7518991	7518991	+	Missense_Mutation	SNP	T	T	A	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	7518991	7518991	TP53	17	T	T	A	49
CDK12	51755	broad.mit.edu	36	17	34881415	34881415	+	Nonsense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10			C	T	C	C	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Nonsense_Mutation	SNP	34881415	34881415	CDK12	17	C	C	T	29
WDR7	23335	broad.mit.edu	36	18	52514569	52514569	+	Missense_Mutation	SNP	A	A	C	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	52514569	52514569	WDR7	18	A	A	C	12
ZSWIM4	65249	broad.mit.edu	36	19	13776878	13776878	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	13776878	13776878	ZSWIM4	19	G	G	T	38
ATP13A1	57130	broad.mit.edu	36	19	19628522	19628522	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	19628522	19628522	ATP13A1	19	G	G	A	39
ZNF43	7594	broad.mit.edu	36	19	21782339	21782339	+	Missense_Mutation	SNP	A	A	C	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	21782339	21782339	ZNF43	19	A	A	C	16
ZNF473	25888	broad.mit.edu	36	19	55241592	55241592	+	Nonsense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Nonsense_Mutation	SNP	55241592	55241592	ZNF473	19	C	C	T	27
SYT3	84258	broad.mit.edu	36	19	55827455	55827455	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	55827455	55827455	SYT3	19	C	C	A	22
ZNF665	79788	broad.mit.edu	36	19	58360782	58360782	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10			C	A	C	C	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Missense_Mutation	SNP	58360782	58360782	ZNF665	19	C	C	A	30
GPR113	165082	broad.mit.edu	36	2	26387192	26387192	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	26387192	26387192	GPR113	2	C	C	G	22
CRNKL1	51340	broad.mit.edu	36	20	19979249	19979249	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10			C	T	C	C	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Silent	SNP	19979249	19979249	CRNKL1	20	C	C	T	23
COMT	1312	broad.mit.edu	36	22	18331093	18331093	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	18331093	18331093	COMT	22	G	G	A	33
SETMAR	6419	broad.mit.edu	36	3	4329990	4329990	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	4329990	4329990	SETMAR	3	G	G	A	37
LRRC3B	116135	broad.mit.edu	36	3	26726762	26726762	+	Missense_Mutation	SNP	A	A	G	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	26726762	26726762	LRRC3B	3	A	A	G	13
SI	6476	broad.mit.edu	36	3	166224101	166224101	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	166224101	166224101	SI	3	G	G	T	36
MECOM	2122	broad.mit.edu	36	3	170316930	170316930	+	Missense_Mutation	SNP	T	T	A	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10			T	A	T	T	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Missense_Mutation	SNP	170316930	170316930	MECOM	3	T	T	A	51
PPARGC1A	10891	broad.mit.edu	36	4	23425162	23425162	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10			C	T	C	C	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Missense_Mutation	SNP	23425162	23425162	PPARGC1A	4	C	C	T	24
SEC31A	22872	broad.mit.edu	36	4	83989074	83989074	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	83989074	83989074	SEC31A	4	C	C	T	19
DCHS2	54798	broad.mit.edu	36	4	155438480	155438480	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	155438480	155438480	DCHS2	4	C	C	G	24
TRIM7	81786	broad.mit.edu	36	5	180559616	180559616	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	180559616	180559616	TRIM7	5	C	C	T	24
HLA-DPB1	3115	broad.mit.edu	36	6	33151827	33151827	+	Silent	SNP	C	C	A	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	33151827	33151827	HLA-DPB1	6	C	C	A	23
T	6862	broad.mit.edu	36	6	166491851	166491851	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	166491851	166491851	T	6	G	G	A	42
CHPF2	54480	broad.mit.edu	36	7	150565627	150565627	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	150565627	150565627	CHPF2	7	C	C	T	31
PEX2	5828	broad.mit.edu	36	8	78058564	78058564	+	Nonsense_Mutation	SNP	T	T	A	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Nonsense_Mutation	SNP	78058564	78058564	PEX2	8	T	T	A	63
FRMD3	257019	broad.mit.edu	36	9	85147995	85147995	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	85147995	85147995	FRMD3	9	C	C	T	22
FAM123B	139285	broad.mit.edu	36	X	63328322	63328322	+	Missense_Mutation	SNP	A	A	T	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10			A	T	A	A	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Missense_Mutation	SNP	63328322	63328322	FAM123B	23	A	A	T	7
CPXCR1	53336	broad.mit.edu	36	X	87895468	87895468	+	Nonsense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Nonsense_Mutation	SNP	87895468	87895468	CPXCR1	23	C	C	T	31
RBMX2	51634	broad.mit.edu	36	X	129370969	129370969	+	Silent	SNP	A	A	G	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	129370969	129370969	RBMX2	23	A	A	G	3
LRIT2	340745	broad.mit.edu	36	10	85972046	85972047	+	Frame_Shift_Ins	INS	-	CC	-	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	Phase_I	Capture	---			Illumina GAIIx	Broad	Frame_Shift_Ins	INS	85972046	85972047	LRIT2	10	-	CC	-	8
BCDIN3D	144233	broad.mit.edu	36	12	48518700	48518700	+	Frame_Shift_Del	DEL	C	-	C	novel	Unknown	TCGA-13-1495-01	TCGA-13-1495-10							Unknown	Unknown	Unknown	Phase_I	Capture	---			Illumina GAIIx	Broad	Frame_Shift_Del	DEL	48518700	48518700	BCDIN3D	12	C	-	C	30
