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 VPS13D 55187 broad.mit.edu 36 1 12325666 12325666 + Missense_Mutation SNP A A C novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 12325666 12325666 VPS13D 1 A A C 4 EPHA2 1969 broad.mit.edu 36 1 16324359 16324359 + Missense_Mutation SNP G G A novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 16324359 16324359 EPHA2 1 G G A 38 USP24 23358 broad.mit.edu 36 1 55397282 55397282 + Missense_Mutation SNP G G C novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55397282 55397282 USP24 1 G G C 43 RSBN1 54665 broad.mit.edu 36 1 114156376 114156376 + Missense_Mutation SNP G G T novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 114156376 114156376 RSBN1 1 G G T 38 CD84 8832 broad.mit.edu 36 1 158801896 158801896 + Missense_Mutation SNP C C T novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 158801896 158801896 CD84 1 C C T 27 C12orf40 283461 broad.mit.edu 36 12 38330387 38330387 + Missense_Mutation SNP C C T novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38330387 38330387 C12orf40 12 C C T 20 SCN8A 6334 broad.mit.edu 36 12 50401812 50401812 + Nonsense_Mutation SNP C C A novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 50401812 50401812 SCN8A 12 C C A 17 TIMELESS 8914 broad.mit.edu 36 12 55113888 55113888 + Missense_Mutation SNP T T A novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 T A T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 55113888 55113888 TIMELESS 12 T T A 54 PLEKHG7 440107 broad.mit.edu 36 12 91672073 91672073 + Missense_Mutation SNP G G A novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 91672073 91672073 PLEKHG7 12 G G A 37 UBE3B 89910 broad.mit.edu 36 12 108452778 108452778 + Missense_Mutation SNP G G T novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 108452778 108452778 UBE3B 12 G G T 36 ZNF268 10795 broad.mit.edu 36 12 132274621 132274621 + Missense_Mutation SNP C C G novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 132274621 132274621 ZNF268 12 C C G 32 ADAD2 161931 broad.mit.edu 36 16 82786063 82786063 + Missense_Mutation SNP C C T novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 82786063 82786063 ADAD2 16 C C T 26 TP53 7157 broad.mit.edu 36 17 7518263 7518263 + Missense_Mutation SNP C C T rs11540652 byHapMap TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7518263 7518263 TP53 17 C C T 23 PNKP 11284 broad.mit.edu 36 19 55057676 55057676 + Missense_Mutation SNP G G T novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55057676 55057676 PNKP 19 G G T 40 CCDC104 112942 broad.mit.edu 36 2 55609605 55609605 + Missense_Mutation SNP G G T novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55609605 55609605 CCDC104 2 G G T 34 UXS1 80146 broad.mit.edu 36 2 106128237 106128237 + Missense_Mutation SNP C C G novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 106128237 106128237 UXS1 2 C C G 19 RBMS1 5937 broad.mit.edu 36 2 161058099 161058099 + Nonsense_Mutation SNP G G A novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 161058099 161058099 RBMS1 2 G G A 46 SP100 6672 broad.mit.edu 36 2 231077183 231077183 + Nonsense_Mutation SNP C C T novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 231077183 231077183 SP100 2 C C T 17 LBP 3929 broad.mit.edu 36 20 36417215 36417215 + Missense_Mutation SNP G G C novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 36417215 36417215 LBP 20 G G C 41 SCN5A 6331 broad.mit.edu 36 3 38621301 38621301 + Missense_Mutation SNP G G A novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38621301 38621301 SCN5A 3 G G A 40 CCDC37 348807 broad.mit.edu 36 3 127637157 127637157 + Missense_Mutation SNP C C T novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 127637157 127637157 CCDC37 3 C C T 27 USP13 8975 broad.mit.edu 36 3 180961631 180961631 + Silent SNP C C G novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 180961631 180961631 USP13 3 C C G 23 B3GNT5 84002 broad.mit.edu 36 3 184470994 184470994 + Nonsense_Mutation SNP C C A novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Nonsense_Mutation SNP 184470994 184470994 B3GNT5 3 C C A 19 MAGEF1 64110 broad.mit.edu 36 3 185912196 185912196 + Silent SNP G G A novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 185912196 185912196 MAGEF1 3 G G A 42 PDLIM5 10611 broad.mit.edu 36 4 95797707 95797707 + Missense_Mutation SNP C C A novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 95797707 95797707 PDLIM5 4 C C A 22 ADAM29 11086 broad.mit.edu 36 4 176133429 176133429 + Missense_Mutation SNP G G A novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 176133429 176133429 ADAM29 4 G G A 35 PLCXD3 345557 broad.mit.edu 36 5 41546284 41546284 + Silent SNP T T A novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 41546284 41546284 PLCXD3 5 T T A 55 LATS1 9113 broad.mit.edu 36 6 150043055 150043055 + Missense_Mutation SNP C C T novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 150043055 150043055 LATS1 6 C C T 27 LAMB1 3912 broad.mit.edu 36 7 107357276 107357276 + Missense_Mutation SNP A A G novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 107357276 107357276 LAMB1 7 A A G 4 KIAA1797 54914 broad.mit.edu 36 9 20875120 20875120 + Missense_Mutation SNP T T A novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 20875120 20875120 KIAA1797 9 T T A 64 MOBKL2B 79817 broad.mit.edu 36 9 27445162 27445162 + Silent SNP G G A novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 27445162 27445162 MOBKL2B 9 G G A 45 PCSK5 5125 broad.mit.edu 36 9 77974504 77974504 + Missense_Mutation SNP G G C novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 77974504 77974504 PCSK5 9 G G C 33 ROR2 4920 broad.mit.edu 36 9 93526859 93526859 + Missense_Mutation SNP C C A novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 93526859 93526859 ROR2 9 C C A 29 OR2K2 26248 broad.mit.edu 36 9 113129786 113129786 + Missense_Mutation SNP T T A novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 113129786 113129786 OR2K2 9 T T A 49 NLGN4X 57502 broad.mit.edu 36 X 5831627 5831627 + Missense_Mutation SNP G G T novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 5831627 5831627 NLGN4X 23 G G T 36 DOCK11 139818 broad.mit.edu 36 X 117590359 117590359 + Missense_Mutation SNP G G C novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 117590359 117590359 DOCK11 23 G G C 33 DDX26B 203522 broad.mit.edu 36 X 134534421 134534421 + Nonsense_Mutation SNP G G T novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 134534421 134534421 DDX26B 23 G G T 33 SPANXN2 494119 broad.mit.edu 36 X 142623233 142623233 + Silent SNP G G T novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 142623233 142623233 SPANXN2 23 G G T 47 TP53BP1 7158 broad.mit.edu 36 15 41555128 41555133 + In_Frame_Del DEL AAGCCA - AAGCCA novel Unknown TCGA-24-1419-01 TCGA-24-1419-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 41555128 41555133 TP53BP1 15 AAGCCA - AAGCCA 9