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