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 RBMXL1 494115 broad.mit.edu 36 1 89221583 89221583 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 89221583 89221583 RBMXL1 1 C C T 27 ARHGAP30 257106 broad.mit.edu 36 1 159289206 159289206 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 159289206 159289206 ARHGAP30 1 C C T 29 TNN 63923 broad.mit.edu 36 1 173329814 173329814 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 173329814 173329814 TNN 1 G G A 41 RYR2 6262 broad.mit.edu 36 1 235560833 235560833 + Silent SNP T T C novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 235560833 235560833 RYR2 1 T T C 63 C10orf18 54906 broad.mit.edu 36 10 5829069 5829069 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 5829069 5829069 C10orf18 10 G G A 35 C10orf137 26098 broad.mit.edu 36 10 127419175 127419175 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 127419175 127419175 C10orf137 10 C C T 25 FAM160A2 84067 broad.mit.edu 36 11 6195856 6195856 + Silent SNP A A C novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 6195856 6195856 FAM160A2 11 A A C 6 ST5 6764 broad.mit.edu 36 11 8674574 8674574 + Missense_Mutation SNP C C G novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 8674574 8674574 ST5 11 C C G 30 C11orf16 56673 broad.mit.edu 36 11 8907627 8907627 + Missense_Mutation SNP A A G novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 8907627 8907627 C11orf16 11 A A G 2 PIK3C2A 5286 broad.mit.edu 36 11 17079488 17079488 + Missense_Mutation SNP A A C novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 17079488 17079488 PIK3C2A 11 A A C 9 EHBP1L1 254102 broad.mit.edu 36 11 65105943 65105943 + Silent SNP A A G novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 65105943 65105943 EHBP1L1 11 A A G 7 IGHMBP2 3508 broad.mit.edu 36 11 68457489 68457490 + Missense_Mutation DNP TC TC GT novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 68457489 68457490 IGHMBP2 11 TC TC GT 54 DSCAML1 57453 broad.mit.edu 36 11 116857947 116857947 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 116857947 116857947 DSCAML1 11 C C T 19 TMPRSS12 283471 broad.mit.edu 36 12 49523911 49523911 + Silent SNP T T A novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 49523911 49523911 TMPRSS12 12 T T A 61 RNASE3 6037 broad.mit.edu 36 14 20429984 20429984 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 20429984 20429984 RNASE3 14 G G A 39 C14orf115 55237 broad.mit.edu 36 14 73894675 73894675 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 73894675 73894675 C14orf115 14 C C T 27 TLN2 83660 broad.mit.edu 36 15 60841913 60841913 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 60841913 60841913 TLN2 15 G G A 37 PALB2 79728 broad.mit.edu 36 16 23554581 23554581 + Nonsense_Mutation SNP C C A novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 23554581 23554581 PALB2 16 C C A 29 PLCG2 5336 broad.mit.edu 36 16 80529930 80529930 + Silent SNP C C G novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 80529930 80529930 PLCG2 16 C C G 21 EIF4A1 1973 broad.mit.edu 36 17 7420652 7420652 + Silent SNP G G A novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 7420652 7420652 EIF4A1 17 G G A 46 CNTD1 124817 broad.mit.edu 36 17 38204617 38204617 + Silent SNP C C T novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 38204617 38204617 CNTD1 17 C C T 19 MYL4 4635 broad.mit.edu 36 17 42654107 42654107 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 42654107 42654107 MYL4 17 G G A 38 ACOX1 51 broad.mit.edu 36 17 71467984 71467984 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 71467984 71467984 ACOX1 17 G G T 45 RPTOR 57521 broad.mit.edu 36 17 76535654 76535654 + Missense_Mutation SNP A A C novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 76535654 76535654 RPTOR 17 A A C 12 LASS4 79603 broad.mit.edu 36 19 8221966 8221966 + Silent SNP G G A novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 8221966 8221966 LASS4 19 G G A 48 MUC16 94025 broad.mit.edu 36 19 8918662 8918662 + Silent SNP G G C novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 8918662 8918662 MUC16 19 G G C 47 UNC13A 23025 broad.mit.edu 36 19 17611681 17611681 + Missense_Mutation SNP T T A novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 17611681 17611681 UNC13A 19 T T A 61 ZNF234 10780 broad.mit.edu 36 19 49353580 49353580 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 49353580 49353580 ZNF234 19 C C A 26 NLRP4 147945 broad.mit.edu 36 19 61061830 61061830 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 61061830 61061830 NLRP4 19 G G A 39 AGBL5 60509 broad.mit.edu 36 2 27145060 27145060 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 27145060 27145060 AGBL5 2 G G T 39 VPS54 51542 broad.mit.edu 36 2 64052843 64052843 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 64052843 64052843 VPS54 2 G G T 41 LRP2 4036 broad.mit.edu 36 2 169812238 169812238 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 169812238 169812238 LRP2 2 G G A 42 USP37 57695 broad.mit.edu 36 2 219107665 219107665 + Missense_Mutation SNP T T A novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 219107665 219107665 USP37 2 T T A 56 GLB1L 79411 broad.mit.edu 36 2 219811305 219811305 + Missense_Mutation SNP T T G novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 219811305 219811305 GLB1L 2 T T G 60 ITM2C 81618 broad.mit.edu 36 2 231450491 231450491 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 231450491 231450491 ITM2C 2 C C A 27 KCNQ2 3785 broad.mit.edu 36 20 61544327 61544327 + Missense_Mutation SNP T T G novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 61544327 61544327 KCNQ2 20 T T G 54 DOPEY2 9980 broad.mit.edu 36 21 36531530 36531530 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 36531530 36531530 DOPEY2 21 C C T 19 CLTCL1 8218 broad.mit.edu 36 22 17621616 17621616 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 17621616 17621616 CLTCL1 22 G G A 47 C3orf58 205428 broad.mit.edu 36 3 145174022 145174022 + Missense_Mutation SNP A A G novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 145174022 145174022 C3orf58 3 A A G 4 FNDC3B 64778 broad.mit.edu 36 3 173563227 173563227 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 173563227 173563227 FNDC3B 3 C C A 28 LIFR 3977 broad.mit.edu 36 5 38546409 38546409 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 38546409 38546409 LIFR 5 C C T 19 PCDHB13 56123 broad.mit.edu 36 5 140575353 140575353 + Missense_Mutation SNP C C G novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 140575353 140575353 PCDHB13 5 C C G 26 ODZ2 57451 broad.mit.edu 36 5 167577995 167577995 + Silent SNP C C T novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 167577995 167577995 ODZ2 5 C C T 19 STK10 6793 broad.mit.edu 36 5 171412610 171412610 + Missense_Mutation SNP T T G novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 171412610 171412610 STK10 5 T T G 60 C6orf136 221545 broad.mit.edu 36 6 30728588 30728588 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 30728588 30728588 C6orf136 6 G G A 48 PPP2R5D 5528 broad.mit.edu 36 6 43086428 43086428 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 43086428 43086428 PPP2R5D 6 G G T 35 ENPP4 22875 broad.mit.edu 36 6 46216070 46216070 + Missense_Mutation SNP A A C novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 A C A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 46216070 46216070 ENPP4 6 A A C 12 USP42 84132 broad.mit.edu 36 7 6156165 6156165 + Silent SNP G G A novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 6156165 6156165 USP42 7 G G A 47 CHRNB3 1142 broad.mit.edu 36 8 42706472 42706472 + Missense_Mutation SNP T T A novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 42706472 42706472 CHRNB3 8 T T A 58 FGD3 89846 broad.mit.edu 36 9 94778675 94778675 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 94778675 94778675 FGD3 9 G G C 43 FCN2 2220 broad.mit.edu 36 9 136918991 136918991 + Missense_Mutation SNP A A G novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 136918991 136918991 FCN2 9 A A G 8 GPM6B 2824 broad.mit.edu 36 X 13702662 13702662 + Silent SNP C C A novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 13702662 13702662 GPM6B 23 C C A 29 MAGEB1 4112 broad.mit.edu 36 X 30179302 30179302 + Silent SNP C C T novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 30179302 30179302 MAGEB1 23 C C T 19 NLGN3 54413 broad.mit.edu 36 X 70306517 70306517 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 70306517 70306517 NLGN3 23 C C T 27 BCORL1 63035 broad.mit.edu 36 X 128975119 128975119 + Silent SNP A A G novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 128975119 128975119 BCORL1 23 A A G 7 ZIC3 7547 broad.mit.edu 36 X 136476579 136476579 + Silent SNP G G A novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 136476579 136476579 ZIC3 23 G G A 38 HJURP 55355 broad.mit.edu 36 2 234419109 234419136 + Splice_Site_Del DEL TTACCTCAAAATACTCTGCACCTTGTAG - TTACCTCAAAATACTCTGCACCTTGTAG novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Splice_Site_Del DEL 234419109 234419136 HJURP 2 TTACCTCAAAATACTCTGCACCTTGTAG - TTACCTCAAAATACTCTGCACCTTGTAG 52 THBS4 7060 broad.mit.edu 36 5 79404846 79404858 + Splice_Site_Del DEL CTTTGCAGTCTGA - CTTTGCAGTCTGA novel Unknown TCGA-13-1477-01 TCGA-13-1477-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Splice_Site_Del DEL 79404846 79404858 THBS4 5 CTTTGCAGTCTGA - CTTTGCAGTCTGA 32