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 DNAJC11 55735 broad.mit.edu 36 1 6619976 6619976 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 6619976 6619976 DNAJC11 1 C C T 19 ALPL 249 broad.mit.edu 36 1 21762289 21762289 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 21762289 21762289 ALPL 1 G G A 34 CCDC28B 79140 broad.mit.edu 36 1 32440214 32440214 + Missense_Mutation SNP A A C novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 32440214 32440214 CCDC28B 1 A A C 14 FAM183A 440585 broad.mit.edu 36 1 43394541 43394541 + Silent SNP G G A novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 43394541 43394541 FAM183A 1 G G A 40 RCOR3 55758 broad.mit.edu 36 1 209552736 209552736 + Missense_Mutation SNP A A G novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 209552736 209552736 RCOR3 1 A A G 2 USH2A 7399 broad.mit.edu 36 1 213874577 213874577 + Silent SNP C C T novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 213874577 213874577 USH2A 1 C C T 31 MYO3A 53904 broad.mit.edu 36 10 26355327 26355327 + Missense_Mutation SNP T T G novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 T G T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 26355327 26355327 MYO3A 10 T T G 52 UNC5B 219699 broad.mit.edu 36 10 72716536 72716536 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 72716536 72716536 UNC5B 10 C C T 23 HABP2 3026 broad.mit.edu 36 10 115327852 115327852 + Missense_Mutation SNP T T G novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 115327852 115327852 HABP2 10 T T G 55 OR51Q1 390061 broad.mit.edu 36 11 5400269 5400269 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 5400269 5400269 OR51Q1 11 G G T 47 FSHB 2488 broad.mit.edu 36 11 30210097 30210097 + Silent SNP C C A novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 30210097 30210097 FSHB 11 C C A 21 QSER1 79832 broad.mit.edu 36 11 32912214 32912214 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 32912214 32912214 QSER1 11 G G A 36 OR8K1 390157 broad.mit.edu 36 11 55870397 55870397 + Missense_Mutation SNP T T C novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55870397 55870397 OR8K1 11 T T C 57 DPF2 5977 broad.mit.edu 36 11 64865046 64865046 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 64865046 64865046 DPF2 11 C C A 26 PUS3 83480 broad.mit.edu 36 11 125270366 125270366 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 125270366 125270366 PUS3 11 G G T 34 CCNT1 904 broad.mit.edu 36 12 47374193 47374193 + Silent SNP A A C novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 47374193 47374193 CCNT1 12 A A C 13 DIP2B 57609 broad.mit.edu 36 12 49378405 49378405 + Silent SNP A A G novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 49378405 49378405 DIP2B 12 A A G 7 PAWR 5074 broad.mit.edu 36 12 78607731 78607731 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 78607731 78607731 PAWR 12 G G T 43 LATS2 26524 broad.mit.edu 36 13 20447312 20447312 + Silent SNP G G T novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 20447312 20447312 LATS2 13 G G T 35 FRY 10129 broad.mit.edu 36 13 31550987 31550987 + Silent SNP C C T novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 31550987 31550987 FRY 13 C C T 19 C14orf43 91748 broad.mit.edu 36 14 73276041 73276041 + Missense_Mutation SNP A A C novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 73276041 73276041 C14orf43 14 A A C 15 NTRK3 4916 broad.mit.edu 36 15 86284908 86284908 + Nonsense_Mutation SNP C C A novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 86284908 86284908 NTRK3 15 C C A 31 CDH8 1006 broad.mit.edu 36 16 60245476 60245476 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 60245476 60245476 CDH8 16 C C T 23 ZFHX3 463 broad.mit.edu 36 16 71380038 71380038 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 71380038 71380038 ZFHX3 16 G G T 39 ANKRD11 29123 broad.mit.edu 36 16 87879044 87879044 + Silent SNP G G A novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 87879044 87879044 ANKRD11 16 G G A 37 TP53 7157 broad.mit.edu 36 17 7518223 7518223 + Splice_Site_SNP SNP C C A novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 7518223 7518223 TP53 17 C C A 18 ZNF560 147741 broad.mit.edu 36 19 9442977 9442977 + Nonsense_Mutation SNP G G A novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Nonsense_Mutation SNP 9442977 9442977 ZNF560 19 G G A 48 ZNF257 113835 broad.mit.edu 36 19 22062936 22062936 + Missense_Mutation SNP T T C novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 22062936 22062936 ZNF257 19 T T C 52 FAM83E 54854 broad.mit.edu 36 19 53808235 53808235 + Silent SNP C C T novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 53808235 53808235 FAM83E 19 C C T 23 ZSWIM2 151112 broad.mit.edu 36 2 187421961 187421961 + Nonsense_Mutation SNP C C A novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 187421961 187421961 ZSWIM2 2 C C A 30 COL4A3 1285 broad.mit.edu 36 2 227855409 227855409 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 227855409 227855409 COL4A3 2 C C T 21 SP100 6672 broad.mit.edu 36 2 231017272 231017272 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 231017272 231017272 SP100 2 G G A 37 KIF16B 55614 broad.mit.edu 36 20 16444271 16444271 + Silent SNP T T A novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 16444271 16444271 KIF16B 20 T T A 51 PLXNB2 23654 broad.mit.edu 36 22 49062153 49062153 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 49062153 49062153 PLXNB2 22 C C T 31 PLXNB2 23654 broad.mit.edu 36 22 49066380 49066380 + Silent SNP C C T novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 49066380 49066380 PLXNB2 22 C C T 24 PLXNB2 23654 broad.mit.edu 36 22 49066760 49066760 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 49066760 49066760 PLXNB2 22 G G T 39 BSN 8927 broad.mit.edu 36 3 49655338 49655338 + Nonsense_Mutation SNP G G T novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 49655338 49655338 BSN 3 G G T 47 MON1A 84315 broad.mit.edu 36 3 49922959 49922959 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 49922959 49922959 MON1A 3 G G A 39 ROPN1 54763 broad.mit.edu 36 3 125178457 125178457 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 125178457 125178457 ROPN1 3 C C A 27 EIF2B5 8893 broad.mit.edu 36 3 185343300 185343300 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 185343300 185343300 EIF2B5 3 G G C 36 ADH5 128 broad.mit.edu 36 4 100212611 100212611 + Nonsense_Mutation SNP G G A novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Nonsense_Mutation SNP 100212611 100212611 ADH5 4 G G A 37 CXXC4 80319 broad.mit.edu 36 4 105631754 105631754 + Missense_Mutation SNP A A G novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 105631754 105631754 CXXC4 4 A A G 8 CDH6 1004 broad.mit.edu 36 5 31335411 31335411 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 31335411 31335411 CDH6 5 G G A 39 PRLR 5618 broad.mit.edu 36 5 35106079 35106079 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 35106079 35106079 PRLR 5 G G A 48 SPZ1 84654 broad.mit.edu 36 5 79652841 79652841 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 79652841 79652841 SPZ1 5 G G C 33 GEMIN5 25929 broad.mit.edu 36 5 154259047 154259047 + Missense_Mutation SNP C C G novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 154259047 154259047 GEMIN5 5 C C G 25 RNF145 153830 broad.mit.edu 36 5 158520861 158520861 + Silent SNP G G A novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 158520861 158520861 RNF145 5 G G A 33 MGAT4B 11282 broad.mit.edu 36 5 179161231 179161231 + Missense_Mutation SNP T T G novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 179161231 179161231 MGAT4B 5 T T G 59 PGBD1 84547 broad.mit.edu 36 6 28372645 28372645 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 28372645 28372645 PGBD1 6 G G A 39 DDO 8528 broad.mit.edu 36 6 110836235 110836235 + Silent SNP T T C novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 110836235 110836235 DDO 6 T T C 49 KIAA1244 57221 broad.mit.edu 36 6 138697573 138697573 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 138697573 138697573 KIAA1244 6 G G A 33 PPP1R3A 5506 broad.mit.edu 36 7 113305739 113305739 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 113305739 113305739 PPP1R3A 7 G G T 33 ANK1 286 broad.mit.edu 36 8 41734807 41734807 + Missense_Mutation SNP A A T novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 A T A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 41734807 41734807 ANK1 8 A A T 8 CSMD3 114788 broad.mit.edu 36 8 113461831 113461831 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 113461831 113461831 CSMD3 8 G G T 40 GPKOW 27238 broad.mit.edu 36 X 48863011 48863011 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 48863011 48863011 GPKOW 23 G G T 44 BRCC3 79184 broad.mit.edu 36 X 153953096 153953096 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 153953096 153953096 BRCC3 23 G G A 36 FAM86B2 653333 broad.mit.edu 36 8 12335964 12335966 + In_Frame_Del DEL CTG - CTG novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 12335964 12335966 FAM86B2 8 CTG - CTG 32 FUT7 2529 broad.mit.edu 36 9 139045318 139045319 + Frame_Shift_Del DEL GA - - novel Unknown TCGA-13-1409-01 TCGA-13-1409-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 139045318 139045319 FUT7 9 GA - - 45