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 KIAA0467 23334 broad.mit.edu 36 1 43686214 43686214 + Missense_Mutation SNP A A T novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 43686214 43686214 KIAA0467 1 A A T 11 NASP 4678 broad.mit.edu 36 1 45853636 45853636 + Missense_Mutation SNP A A G novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 45853636 45853636 NASP 1 A A G 3 ZZZ3 26009 broad.mit.edu 36 1 77870155 77870155 + Silent SNP T T C novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 77870155 77870155 ZZZ3 1 T T C 52 IQGAP3 128239 broad.mit.edu 36 1 154773631 154773631 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 154773631 154773631 IQGAP3 1 G G C 35 F11R 50848 broad.mit.edu 36 1 159257448 159257448 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 159257448 159257448 F11R 1 G G A 35 TNN 63923 broad.mit.edu 36 1 173315944 173315944 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 173315944 173315944 TNN 1 G G C 34 LHX4 89884 broad.mit.edu 36 1 178507763 178507763 + Silent SNP A A T novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 178507763 178507763 LHX4 1 A A T 11 TTC13 79573 broad.mit.edu 36 1 229127284 229127284 + Silent SNP C C T novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 229127284 229127284 TTC13 1 C C T 31 TRIM67 440730 broad.mit.edu 36 1 229417775 229417775 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 229417775 229417775 TRIM67 1 C C A 20 ZNF238 10472 broad.mit.edu 36 1 242284516 242284516 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 242284516 242284516 ZNF238 1 G G A 40 ZFYVE27 118813 broad.mit.edu 36 10 99500132 99500132 + Missense_Mutation SNP A A G novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 99500132 99500132 ZFYVE27 10 A A G 11 PDCD11 22984 broad.mit.edu 36 10 105168268 105168268 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 105168268 105168268 PDCD11 10 C C T 22 CTTN 2017 broad.mit.edu 36 11 69946724 69946724 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 69946724 69946724 CTTN 11 G G C 43 HOXC8 3224 broad.mit.edu 36 12 52691424 52691424 + Missense_Mutation SNP A A C novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 52691424 52691424 HOXC8 12 A A C 5 FAM109A 144717 broad.mit.edu 36 12 110285217 110285218 + Missense_Mutation DNP CC CC AT novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 110285217 110285218 FAM109A 12 CC CC AT 22 ATP8A2 51761 broad.mit.edu 36 13 25484707 25484707 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 25484707 25484707 ATP8A2 13 G G A 39 VPS13C 54832 broad.mit.edu 36 15 59954389 59954389 + Missense_Mutation SNP T T A novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 59954389 59954389 VPS13C 15 T T A 62 GTF3C1 2975 broad.mit.edu 36 16 27457177 27457177 + Missense_Mutation SNP A A C novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 27457177 27457177 GTF3C1 16 A A C 6 SLC38A7 55238 broad.mit.edu 36 16 57271478 57271478 + Silent SNP A A G novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 57271478 57271478 SLC38A7 16 A A G 8 TP53 7157 broad.mit.edu 36 17 7517845 7517845 + Missense_Mutation SNP C C A rs28934576 Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7517845 7517845 TP53 17 C C A 19 STAT5B 6777 broad.mit.edu 36 17 37633087 37633087 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 37633087 37633087 STAT5B 17 C C A 25 FAM117A 81558 broad.mit.edu 36 17 45149912 45149912 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 45149912 45149912 FAM117A 17 C C A 18 CHAD 1101 broad.mit.edu 36 17 45898070 45898070 + Missense_Mutation SNP C C T rs35218093 byCluster;byFrequency TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 45898070 45898070 CHAD 17 C C T 23 ZNF521 25925 broad.mit.edu 36 18 21058980 21058980 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 21058980 21058980 ZNF521 18 C C T 23 MUC16 94025 broad.mit.edu 36 19 8838643 8838643 + Missense_Mutation SNP T T C novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 8838643 8838643 MUC16 19 T T C 60 PKN1 5585 broad.mit.edu 36 19 14423650 14423650 + Missense_Mutation SNP A A G novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 14423650 14423650 PKN1 19 A A G 11 FBL 2091 broad.mit.edu 36 19 45023138 45023138 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 45023138 45023138 FBL 19 C C A 30 SPTBN4 57731 broad.mit.edu 36 19 45764084 45764084 + Silent SNP C C T novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 45764084 45764084 SPTBN4 19 C C T 28 AXL 558 broad.mit.edu 36 19 46417207 46417207 + Missense_Mutation SNP T T G novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 46417207 46417207 AXL 19 T T G 59 ARHGEF1 9138 broad.mit.edu 36 19 47080381 47080381 + Missense_Mutation SNP T T A novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 47080381 47080381 ARHGEF1 19 T T A 62 SCN3A 6328 broad.mit.edu 36 2 165656048 165656048 + Nonsense_Mutation SNP G G A novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Nonsense_Mutation SNP 165656048 165656048 SCN3A 2 G G A 39 TMEM198 130612 broad.mit.edu 36 2 220120642 220120642 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 220120642 220120642 TMEM198 2 G G T 36 SIRPA 140885 broad.mit.edu 36 20 1851108 1851108 + Missense_Mutation SNP G G A rs2422666 byCluster;byFrequency;byHapMap TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 1851108 1851108 SIRPA 20 G G A 40 PCSK2 5126 broad.mit.edu 36 20 17382587 17382587 + Missense_Mutation SNP C C G novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 17382587 17382587 PCSK2 20 C C G 18 DIDO1 11083 broad.mit.edu 36 20 60982318 60982318 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 60982318 60982318 DIDO1 20 G G A 37 DIDO1 11083 broad.mit.edu 36 20 61011659 61011659 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 61011659 61011659 DIDO1 20 G G A 46 UMODL1 89766 broad.mit.edu 36 21 42383593 42383593 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 42383593 42383593 UMODL1 21 C C T 19 NUP210 23225 broad.mit.edu 36 3 13353308 13353308 + Silent SNP G G A novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 13353308 13353308 NUP210 3 G G A 44 TM4SF18 116441 broad.mit.edu 36 3 150525433 150525433 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 150525433 150525433 TM4SF18 3 C C T 25 PIK3CA 5290 broad.mit.edu 36 3 180425287 180425287 + Silent SNP C C A novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 180425287 180425287 PIK3CA 3 C C A 32 TACC3 10460 broad.mit.edu 36 4 1699370 1699370 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 1699370 1699370 TACC3 4 C C T 26 SFRP2 6423 broad.mit.edu 36 4 154922125 154922125 + Silent SNP C C G novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 154922125 154922125 SFRP2 4 C C G 23 CEP120 153241 broad.mit.edu 36 5 122752141 122752141 + Silent SNP T T C novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 122752141 122752141 CEP120 5 T T C 56 SEPT8 23176 broad.mit.edu 36 5 132124565 132124565 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 132124565 132124565 SEPT8 5 G G T 46 CCDC69 26112 broad.mit.edu 36 5 150565218 150565218 + Missense_Mutation SNP T T A novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 150565218 150565218 CCDC69 5 T T A 60 HERV-FRD 405754 broad.mit.edu 36 6 11213451 11213451 + Missense_Mutation SNP T T C novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 11213451 11213451 HERV-FRD 6 T T C 64 TRIM26 7726 broad.mit.edu 36 6 30272364 30272364 + Missense_Mutation SNP T T G novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 30272364 30272364 TRIM26 6 T T G 63 RUNX2 860 broad.mit.edu 36 6 45588070 45588070 + Silent SNP C C A novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 45588070 45588070 RUNX2 6 C C A 21 THSD7A 221981 broad.mit.edu 36 7 11642734 11642734 + Silent SNP A A C novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 11642734 11642734 THSD7A 7 A A C 3 NT5C3 51251 broad.mit.edu 36 7 33023709 33023709 + Missense_Mutation SNP A A T novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 A T A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 33023709 33023709 NT5C3 7 A A T 11 PEX1 5189 broad.mit.edu 36 7 91985096 91985096 + Silent SNP C C T novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 91985096 91985096 PEX1 7 C C T 21 CCDC132 55610 broad.mit.edu 36 7 92764000 92764000 + Missense_Mutation SNP T T G novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 92764000 92764000 CCDC132 7 T T G 53 SCARA3 51435 broad.mit.edu 36 8 27584534 27584534 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 27584534 27584534 SCARA3 8 G G C 42 BAG4 9530 broad.mit.edu 36 8 38187027 38187027 + Silent SNP T T A novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 38187027 38187027 BAG4 8 T T A 62 NAPRT1 93100 broad.mit.edu 36 8 144728546 144728546 + Silent SNP G G C novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 144728546 144728546 NAPRT1 8 G G C 43 C9orf41 138199 broad.mit.edu 36 9 76821115 76821115 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 76821115 76821115 C9orf41 9 G G A 41 COL5A1 1289 broad.mit.edu 36 9 136857473 136857473 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 136857473 136857473 COL5A1 9 G G A 37 IRAK1 3654 broad.mit.edu 36 X 152931859 152931859 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 152931859 152931859 IRAK1 23 C C T 30 SPRR1B 6699 broad.mit.edu 36 1 151271566 151271637 + In_Frame_Del DEL TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA - TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 151271566 151271637 SPRR1B 1 TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA - TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA 55 ELMO3 79767 broad.mit.edu 36 16 65792082 65792087 + In_Frame_Del DEL AACCTC - AACCTC novel Unknown TCGA-13-1512-01 TCGA-13-1512-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 65792082 65792087 ELMO3 16 AACCTC - AACCTC 9