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 EFNA4 1945 broad.mit.edu 36 1 153308043 153308043 + Missense_Mutation SNP T T C novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 153308043 153308043 EFNA4 1 T T C 63 DUSP27 92235 broad.mit.edu 36 1 165362394 165362394 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 165362394 165362394 DUSP27 1 G G A 38 NLRP3 114548 broad.mit.edu 36 1 245654785 245654785 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 245654785 245654785 NLRP3 1 G G A 42 UPF2 26019 broad.mit.edu 36 10 12041243 12041243 + Missense_Mutation SNP C C T novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 12041243 12041243 UPF2 10 C C T 19 TET1 80312 broad.mit.edu 36 10 70121233 70121233 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 70121233 70121233 TET1 10 G G A 46 CCAR1 55749 broad.mit.edu 36 10 70217784 70217784 + Missense_Mutation SNP C C T novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 70217784 70217784 CCAR1 10 C C T 32 ZNF511 118472 broad.mit.edu 36 10 134973378 134973378 + Silent SNP C C T novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 134973378 134973378 ZNF511 10 C C T 25 SHISA2 387914 broad.mit.edu 36 13 25518663 25518663 + Silent SNP C C T novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 25518663 25518663 SHISA2 13 C C T 23 CGNL1 84952 broad.mit.edu 36 15 55517809 55517809 + Missense_Mutation SNP C C T novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55517809 55517809 CGNL1 15 C C T 21 MCTP2 55784 broad.mit.edu 36 15 92711912 92711912 + Missense_Mutation SNP G G T novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 92711912 92711912 MCTP2 15 G G T 43 DCUN1D3 123879 broad.mit.edu 36 16 20778769 20778769 + Silent SNP C C T novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 20778769 20778769 DCUN1D3 16 C C T 22 NLRC5 84166 broad.mit.edu 36 16 55627576 55627576 + Silent SNP G G A novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 55627576 55627576 NLRC5 16 G G A 46 TUBB3 10381 broad.mit.edu 36 16 88529263 88529263 + Silent SNP C C T novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 88529263 88529263 TUBB3 16 C C T 23 ITGAE 3682 broad.mit.edu 36 17 3598010 3598010 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 3598010 3598010 ITGAE 17 G G A 39 TP53 7157 broad.mit.edu 36 17 7517622 7517622 + Nonsense_Mutation SNP G G A novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Nonsense_Mutation SNP 7517622 7517622 TP53 17 G G A 47 DHX8 1659 broad.mit.edu 36 17 38925628 38925628 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38925628 38925628 DHX8 17 G G A 37 CBX8 57332 broad.mit.edu 36 17 75383403 75383403 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 75383403 75383403 CBX8 17 G G A 43 MEP1B 4225 broad.mit.edu 36 18 28041333 28041333 + Missense_Mutation SNP C C T novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 28041333 28041333 MEP1B 18 C C T 17 C19orf47 126526 broad.mit.edu 36 19 45526256 45526256 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 45526256 45526256 C19orf47 19 G G A 41 ZNF331 55422 broad.mit.edu 36 19 58772204 58772204 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 58772204 58772204 ZNF331 19 G G A 43 EGR4 1961 broad.mit.edu 36 2 73372938 73372938 + Missense_Mutation SNP C C T novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 73372938 73372938 EGR4 2 C C T 27 SLC4A5 57835 broad.mit.edu 36 2 74313134 74313134 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 74313134 74313134 SLC4A5 2 G G A 35 SCN2A 6326 broad.mit.edu 36 2 165907090 165907090 + Missense_Mutation SNP G G T novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 165907090 165907090 SCN2A 2 G G T 33 FAM171B 165215 broad.mit.edu 36 2 187324232 187324232 + Missense_Mutation SNP G G C novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 187324232 187324232 FAM171B 2 G G C 36 PLTP 5360 broad.mit.edu 36 20 43971666 43971666 + Silent SNP A A C novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 43971666 43971666 PLTP 20 A A C 7 CD40 958 broad.mit.edu 36 20 44184735 44184735 + Silent SNP G G A novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 44184735 44184735 CD40 20 G G A 37 SON 6651 broad.mit.edu 36 21 33847128 33847128 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 33847128 33847128 SON 21 G G A 36 BAP1 8314 broad.mit.edu 36 3 52415413 52415413 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 52415413 52415413 BAP1 3 G G A 39 CRIPAK 285464 broad.mit.edu 36 4 1379118 1379118 + Silent SNP G G A novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 1379118 1379118 CRIPAK 4 G G A 40 THAP9 79725 broad.mit.edu 36 4 84057373 84057373 + Silent SNP T T C novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 84057373 84057373 THAP9 4 T T C 57 PLA2G12A 81579 broad.mit.edu 36 4 110859322 110859322 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 110859322 110859322 PLA2G12A 4 G G A 39 MAB21L2 10586 broad.mit.edu 36 4 151724424 151724424 + Missense_Mutation SNP C C A novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 151724424 151724424 MAB21L2 4 C C A 18 KIF2A 3796 broad.mit.edu 36 5 61704091 61704091 + Silent SNP C C T novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 61704091 61704091 KIF2A 5 C C T 32 PCDHA13 56136 broad.mit.edu 36 5 140242751 140242751 + Silent SNP C C T novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 140242751 140242751 PCDHA13 5 C C T 19 HIST1H2BD 3017 broad.mit.edu 36 6 26266441 26266441 + Missense_Mutation SNP C C G novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 26266441 26266441 HIST1H2BD 6 C C G 28 ZFP57 346171 broad.mit.edu 36 6 29748981 29748981 + Silent SNP T T G novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 29748981 29748981 ZFP57 6 T T G 54 MAPK14 1432 broad.mit.edu 36 6 36103942 36103942 + Silent SNP G G C novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 36103942 36103942 MAPK14 6 G G C 42 OPRM1 4988 broad.mit.edu 36 6 154452831 154452831 + Silent SNP C C T novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 154452831 154452831 OPRM1 6 C C T 25 TNS3 64759 broad.mit.edu 36 7 47417873 47417873 + Nonsense_Mutation SNP G G A novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 47417873 47417873 TNS3 7 G G A 47 AKAP9 10142 broad.mit.edu 36 7 91547318 91547318 + Missense_Mutation SNP A A T novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 A T A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 91547318 91547318 AKAP9 7 A A T 2 ORAI2 80228 broad.mit.edu 36 7 101866527 101866527 + Missense_Mutation SNP C C T novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 101866527 101866527 ORAI2 7 C C T 32 SNTG1 54212 broad.mit.edu 36 8 51611850 51611850 + Nonsense_Mutation SNP G G A novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 51611850 51611850 SNTG1 8 G G A 44 ZNF7 7553 broad.mit.edu 36 8 146038866 146038866 + Missense_Mutation SNP C C T novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 146038866 146038866 ZNF7 8 C C T 26 ACRC 93953 broad.mit.edu 36 X 70740618 70740618 + Missense_Mutation SNP G G A novel Unknown TCGA-13-0899-01 TCGA-13-0899-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 70740618 70740618 ACRC 23 G G A 37