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 LYPLA2 11313 broad.mit.edu 36 1 23993658 23993658 + Missense_Mutation SNP T T C novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 23993658 23993658 LYPLA2 1 T T C 51 CD1B 910 broad.mit.edu 36 1 156565384 156565384 + Missense_Mutation SNP G G A novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 156565384 156565384 CD1B 1 G G A 42 DPT 1805 broad.mit.edu 36 1 166950153 166950153 + Missense_Mutation SNP C C G novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 166950153 166950153 DPT 1 C C G 31 HMCN1 83872 broad.mit.edu 36 1 184100339 184100339 + Missense_Mutation SNP C C A novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 184100339 184100339 HMCN1 1 C C A 28 DENND1B 163486 broad.mit.edu 36 1 195747698 195747698 + Splice_Site_SNP SNP C C T novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 195747698 195747698 DENND1B 1 C C T 24 SUV39H2 79723 broad.mit.edu 36 10 14979166 14979166 + Missense_Mutation SNP C C G novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 14979166 14979166 SUV39H2 10 C C G 22 SORBS1 10580 broad.mit.edu 36 10 97086835 97086835 + Silent SNP T T A novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 97086835 97086835 SORBS1 10 T T A 59 CDON 50937 broad.mit.edu 36 11 125398520 125398520 + Missense_Mutation SNP G G C novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 125398520 125398520 CDON 11 G G C 33 NECAP1 25977 broad.mit.edu 36 12 8136905 8136905 + Silent SNP A A G novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 8136905 8136905 NECAP1 12 A A G 11 SCN8A 6334 broad.mit.edu 36 12 50470514 50470514 + Silent SNP G G C novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 50470514 50470514 SCN8A 12 G G C 47 NBEA 26960 broad.mit.edu 36 13 34513220 34513220 + Missense_Mutation SNP C C T novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 34513220 34513220 NBEA 13 C C T 31 LRRK1 79705 broad.mit.edu 36 15 99410657 99410657 + Missense_Mutation SNP C C G novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 99410657 99410657 LRRK1 15 C C G 24 PALB2 79728 broad.mit.edu 36 16 23553912 23553912 + Missense_Mutation SNP T T C novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 T C T T Unknown Valid Somatic x x 454_PCR_WGA x Broad Missense_Mutation SNP 23553912 23553912 PALB2 16 T T C 61 SNX20 124460 broad.mit.edu 36 16 49268884 49268884 + Missense_Mutation SNP A A G novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 49268884 49268884 SNX20 16 A A G 6 MMP2 4313 broad.mit.edu 36 16 54081185 54081185 + Silent SNP G G A novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 54081185 54081185 MMP2 16 G G A 37 TP53 7157 broad.mit.edu 36 17 7518261 7518261 + Missense_Mutation SNP T T C rs67185453 Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7518261 7518261 TP53 17 T T C 54 CDK12 51755 broad.mit.edu 36 17 34929759 34929759 + Missense_Mutation SNP A A T novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 A T A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 34929759 34929759 CDK12 17 A A T 16 DLGAP1 9229 broad.mit.edu 36 18 3869507 3869507 + Missense_Mutation SNP G G A novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 3869507 3869507 DLGAP1 18 G G A 38 ZNF536 9745 broad.mit.edu 36 19 35626726 35626726 + Silent SNP C C T novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 35626726 35626726 ZNF536 19 C C T 30 ZSWIM3 140831 broad.mit.edu 36 20 43940621 43940621 + Missense_Mutation SNP C C T novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 43940621 43940621 ZSWIM3 20 C C T 23 KRTAP10-9 386676 broad.mit.edu 36 21 44872235 44872235 + Missense_Mutation SNP G G A novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 44872235 44872235 KRTAP10-9 21 G G A 35 IQSEC1 9922 broad.mit.edu 36 3 12932152 12932152 + Missense_Mutation SNP T T C novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 12932152 12932152 IQSEC1 3 T T C 52 SEMA3G 56920 broad.mit.edu 36 3 52447095 52447095 + Missense_Mutation SNP C C T novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 52447095 52447095 SEMA3G 3 C C T 27 SI 6476 broad.mit.edu 36 3 166267825 166267825 + Missense_Mutation SNP G G A novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 166267825 166267825 SI 3 G G A 36 PIGG 54872 broad.mit.edu 36 4 505043 505043 + Missense_Mutation SNP G G A novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 505043 505043 PIGG 4 G G A 43 ANP32C 23520 broad.mit.edu 36 4 165337616 165337616 + Missense_Mutation SNP C C T novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 165337616 165337616 ANP32C 4 C C T 31 CDH18 1016 broad.mit.edu 36 5 19519330 19519330 + Silent SNP A A T novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 19519330 19519330 CDH18 5 A A T 6 EPB41L4A 64097 broad.mit.edu 36 5 111532600 111532600 + Missense_Mutation SNP G G A novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 111532600 111532600 EPB41L4A 5 G G A 37 AFF4 27125 broad.mit.edu 36 5 132298123 132298123 + Missense_Mutation SNP G G C novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 132298123 132298123 AFF4 5 G G C 33 FLT4 2324 broad.mit.edu 36 5 179981457 179981457 + Missense_Mutation SNP C C T novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 179981457 179981457 FLT4 5 C C T 22 GCNT2 2651 broad.mit.edu 36 6 10664686 10664686 + Missense_Mutation SNP G G A rs55786982 Unknown TCGA-24-1466-01 TCGA-24-1466-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 10664686 10664686 GCNT2 6 G G A 36 HIST1H3B 8358 broad.mit.edu 36 6 26139918 26139918 + Missense_Mutation SNP C C T novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 26139918 26139918 HIST1H3B 6 C C T 31 HLA-E 3133 broad.mit.edu 36 6 30565666 30565666 + Silent SNP G G A novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 30565666 30565666 HLA-E 6 G G A 43 GPR115 221393 broad.mit.edu 36 6 47788128 47788128 + Missense_Mutation SNP A A G novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 47788128 47788128 GPR115 6 A A G 11 FAM83B 222584 broad.mit.edu 36 6 54912525 54912525 + Missense_Mutation SNP T T C novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 54912525 54912525 FAM83B 6 T T C 60 KCNQ5 56479 broad.mit.edu 36 6 73843871 73843871 + Missense_Mutation SNP G G A novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 73843871 73843871 KCNQ5 6 G G A 38 FIGNL1 63979 broad.mit.edu 36 7 50482427 50482427 + Missense_Mutation SNP T T A novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 50482427 50482427 FIGNL1 7 T T A 57 COBL 23242 broad.mit.edu 36 7 51063831 51063831 + Missense_Mutation SNP T T G novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 51063831 51063831 COBL 7 T T G 56 AKAP9 10142 broad.mit.edu 36 7 91550465 91550465 + Missense_Mutation SNP G G T novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 91550465 91550465 AKAP9 7 G G T 36 SGCE 8910 broad.mit.edu 36 7 94086198 94086198 + Missense_Mutation SNP G G A novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 94086198 94086198 SGCE 7 G G A 39 MLL5 55904 broad.mit.edu 36 7 104536839 104536839 + Missense_Mutation SNP C C G novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 104536839 104536839 MLL5 7 C C G 32 KIAA1549 57670 broad.mit.edu 36 7 138253089 138253089 + Missense_Mutation SNP C C T novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 138253089 138253089 KIAA1549 7 C C T 19 PCM1 5108 broad.mit.edu 36 8 17857267 17857267 + Missense_Mutation SNP C C G novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 17857267 17857267 PCM1 8 C C G 17 ZFHX4 79776 broad.mit.edu 36 8 77924389 77924389 + Silent SNP G G T novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 77924389 77924389 ZFHX4 8 G G T 39 NDRG1 10397 broad.mit.edu 36 8 134365720 134365720 + Missense_Mutation SNP T T C novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 134365720 134365720 NDRG1 8 T T C 55 MPDZ 8777 broad.mit.edu 36 9 13214504 13214504 + Missense_Mutation SNP G G C novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 13214504 13214504 MPDZ 9 G G C 33 C9orf79 286234 broad.mit.edu 36 9 89691825 89691825 + Missense_Mutation SNP C C T novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 89691825 89691825 C9orf79 9 C C T 23 SPTAN1 6709 broad.mit.edu 36 9 130428779 130428779 + Missense_Mutation SNP A A G novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 130428779 130428779 SPTAN1 9 A A G 4 FRMPD4 9758 broad.mit.edu 36 X 12622478 12622478 + Missense_Mutation SNP A A G novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 12622478 12622478 FRMPD4 23 A A G 11 LAS1L 81887 broad.mit.edu 36 X 64660209 64660209 + Silent SNP G G A novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 64660209 64660209 LAS1L 23 G G A 35 PHKA1 5255 broad.mit.edu 36 X 71781000 71781000 + Missense_Mutation SNP C C A novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 71781000 71781000 PHKA1 23 C C A 25 NAV1 89796 broad.mit.edu 36 1 200016216 200016219 + Frame_Shift_Del DEL CAGA - CAGA novel Unknown TCGA-24-1466-01 TCGA-24-1466-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 200016216 200016219 NAV1 1 CAGA - CAGA 29