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 PLOD1 5351 broad.mit.edu 36 1 11941249 11941249 + Silent SNP C C T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 11941249 11941249 PLOD1 1 C C T 30 GRIK3 2899 broad.mit.edu 36 1 37119018 37119018 + Silent SNP G G A novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 37119018 37119018 GRIK3 1 G G A 47 LRRC41 10489 broad.mit.edu 36 1 46517267 46517267 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 46517267 46517267 LRRC41 1 G G A 45 CDKN2C 1031 broad.mit.edu 36 1 51212213 51212213 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 51212213 51212213 CDKN2C 1 G G A 37 LRRIQ3 127255 broad.mit.edu 36 1 74420873 74420873 + Silent SNP A A G novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 74420873 74420873 LRRIQ3 1 A A G 9 KDM5B 10765 broad.mit.edu 36 1 200981711 200981711 + Missense_Mutation SNP G G T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 200981711 200981711 KDM5B 1 G G T 33 IL2RA 3559 broad.mit.edu 36 10 6103503 6103503 + Missense_Mutation SNP C C T rs55841382 Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 6103503 6103503 IL2RA 10 C C T 24 NLRP10 338322 broad.mit.edu 36 11 7941477 7941477 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7941477 7941477 NLRP10 11 C C T 30 TRIM44 54765 broad.mit.edu 36 11 35663409 35663410 + Missense_Mutation DNP CG CG TT novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 35663409 35663410 TRIM44 11 CG CG TT 23 SORL1 6653 broad.mit.edu 36 11 120962233 120962233 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 120962233 120962233 SORL1 11 G G A 37 OR10G8 219869 broad.mit.edu 36 11 123406421 123406421 + Silent SNP G G T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 123406421 123406421 OR10G8 11 G G T 45 KIRREL3 84623 broad.mit.edu 36 11 125812085 125812085 + Missense_Mutation SNP C C A novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 125812085 125812085 KIRREL3 11 C C A 20 NFRKB 4798 broad.mit.edu 36 11 129245037 129245037 + Silent SNP G G A novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 129245037 129245037 NFRKB 11 G G A 43 NRIP2 83714 broad.mit.edu 36 12 2814317 2814317 + Missense_Mutation SNP C C G novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 2814317 2814317 NRIP2 12 C C G 32 SLC16A7 9194 broad.mit.edu 36 12 58455155 58455155 + Missense_Mutation SNP A A G novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 58455155 58455155 SLC16A7 12 A A G 16 POLE 5426 broad.mit.edu 36 12 131730604 131730604 + Silent SNP G G A novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 131730604 131730604 POLE 12 G G A 33 FAM71D 161142 broad.mit.edu 36 14 66741163 66741163 + Silent SNP C C T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 66741163 66741163 FAM71D 14 C C T 22 OR4N4 283694 broad.mit.edu 36 15 19883929 19883929 + Silent SNP C C A novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 19883929 19883929 OR4N4 15 C C A 32 NOD2 64127 broad.mit.edu 36 16 49291059 49291059 + Missense_Mutation SNP G G C novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 49291059 49291059 NOD2 16 G G C 42 EDC4 23644 broad.mit.edu 36 16 66473166 66473166 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 66473166 66473166 EDC4 16 G G A 40 KARS 3735 broad.mit.edu 36 16 74220011 74220011 + Missense_Mutation SNP A A T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 74220011 74220011 KARS 16 A A T 4 TP53 7157 broad.mit.edu 36 17 7517842 7517842 + Missense_Mutation SNP A A C novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7517842 7517842 TP53 17 A A C 2 EFNB3 1949 broad.mit.edu 36 17 7552491 7552491 + Silent SNP G G C novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 7552491 7552491 EFNB3 17 G G C 41 C18orf22 79863 broad.mit.edu 36 18 75899510 75899510 + Missense_Mutation SNP C C A novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 75899510 75899510 C18orf22 18 C C A 20 FAM129C 199786 broad.mit.edu 36 19 17523661 17523661 + Missense_Mutation SNP T T C novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 17523661 17523661 FAM129C 19 T T C 50 ECH1 1891 broad.mit.edu 36 19 44013967 44013967 + Missense_Mutation SNP T T C novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 44013967 44013967 ECH1 19 T T C 55 ZNF582 147948 broad.mit.edu 36 19 61587438 61587438 + Missense_Mutation SNP C C A novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 61587438 61587438 ZNF582 19 C C A 32 ALLC 55821 broad.mit.edu 36 2 3707143 3707143 + Missense_Mutation SNP G G C novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 3707143 3707143 ALLC 2 G G C 46 GREB1 9687 broad.mit.edu 36 2 11672796 11672796 + Missense_Mutation SNP A A T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 11672796 11672796 GREB1 2 A A T 2 TTN 7273 broad.mit.edu 36 2 179337195 179337195 + Silent SNP A A T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 179337195 179337195 TTN 2 A A T 3 RBM12 10137 broad.mit.edu 36 20 33705462 33705462 + Silent SNP T T C novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 33705462 33705462 RBM12 20 T T C 58 ZBP1 81030 broad.mit.edu 36 20 55623407 55623407 + Missense_Mutation SNP C C G novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55623407 55623407 ZBP1 20 C C G 32 ITGB2 3689 broad.mit.edu 36 21 45136247 45136247 + Silent SNP C C T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 45136247 45136247 ITGB2 21 C C T 25 GGTLC2 91227 broad.mit.edu 36 22 21319329 21319329 + Silent SNP A A T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 21319329 21319329 GGTLC2 22 A A T 6 CCDC157 550631 broad.mit.edu 36 22 29092086 29092086 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 29092086 29092086 CCDC157 22 G G A 39 SETD2 29072 broad.mit.edu 36 3 47073750 47073750 + Nonsense_Mutation SNP A A T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 47073750 47073750 SETD2 3 A A T 8 COL7A1 1294 broad.mit.edu 36 3 48600780 48600780 + Silent SNP C C T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 48600780 48600780 COL7A1 3 C C T 29 PODXL2 50512 broad.mit.edu 36 3 128862576 128862576 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 128862576 128862576 PODXL2 3 G G A 47 GPR149 344758 broad.mit.edu 36 3 155538753 155538753 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 155538753 155538753 GPR149 3 C C T 19 PEX5L 51555 broad.mit.edu 36 3 181010092 181010092 + Missense_Mutation SNP T T C novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 181010092 181010092 PEX5L 3 T T C 57 ECE2 9718 broad.mit.edu 36 3 185489944 185489944 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 185489944 185489944 ECE2 3 G G A 39 PCDHB12 56124 broad.mit.edu 36 5 140570171 140570171 + Missense_Mutation SNP T T G novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 140570171 140570171 PCDHB12 5 T T G 55 ABLIM3 22885 broad.mit.edu 36 5 148607627 148607627 + Missense_Mutation SNP C C A novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 148607627 148607627 ABLIM3 5 C C A 28 OR2W1 26692 broad.mit.edu 36 6 29120568 29120568 + Missense_Mutation SNP G G T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 29120568 29120568 OR2W1 6 G G T 37 MED23 9439 broad.mit.edu 36 6 131950541 131950541 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 131950541 131950541 MED23 6 C C T 18 TAAR8 83551 broad.mit.edu 36 6 132915641 132915641 + Silent SNP C C T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 132915641 132915641 TAAR8 6 C C T 28 RSPH3 83861 broad.mit.edu 36 6 159321911 159321911 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 159321911 159321911 RSPH3 6 C C T 31 CRHR2 1395 broad.mit.edu 36 7 30661826 30661826 + Silent SNP C C T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 30661826 30661826 CRHR2 7 C C T 25 MOGAT3 346606 broad.mit.edu 36 7 100625957 100625957 + Missense_Mutation SNP G G T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 100625957 100625957 MOGAT3 7 G G T 44 CCDC136 64753 broad.mit.edu 36 7 128233162 128233162 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 128233162 128233162 CCDC136 7 C C T 31 ATG9B 285973 broad.mit.edu 36 7 150349221 150349221 + Missense_Mutation SNP A A T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 150349221 150349221 ATG9B 7 A A T 7 BMP1 649 broad.mit.edu 36 8 22120416 22120416 + Missense_Mutation SNP A A T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 22120416 22120416 BMP1 8 A A T 6 ZFHX4 79776 broad.mit.edu 36 8 77780713 77780713 + Missense_Mutation SNP G G T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 77780713 77780713 ZFHX4 8 G G T 42 MTBP 27085 broad.mit.edu 36 8 121600187 121600187 + Silent SNP T T C novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 121600187 121600187 MTBP 8 T T C 60 SMC5 23137 broad.mit.edu 36 9 72087265 72087265 + Silent SNP A A T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 72087265 72087265 SMC5 9 A A T 9 TTF1 7270 broad.mit.edu 36 9 134253418 134253418 + Missense_Mutation SNP C C A novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 134253418 134253418 TTF1 9 C C A 32 FAM47A 158724 broad.mit.edu 36 X 34058268 34058268 + Silent SNP C C T novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 34058268 34058268 FAM47A 23 C C T 31 PAPPA2 60676 broad.mit.edu 36 1 175027208 175027217 + Frame_Shift_Del DEL GTGGAGTACA - GTGGAGTACA novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 175027208 175027217 PAPPA2 1 GTGGAGTACA - GTGGAGTACA 48 ETFDH 2110 broad.mit.edu 36 4 159847245 159847254 + Frame_Shift_Del DEL CGGCTCAAGC - CGGCTCAAGC novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 159847245 159847254 ETFDH 4 CGGCTCAAGC - CGGCTCAAGC 19 PCDHGC3 5098 broad.mit.edu 36 5 140836006 140836014 + In_Frame_Del DEL GTGGGCAAC - GTGGGCAAC novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 140836006 140836014 PCDHGC3 5 GTGGGCAAC - GTGGGCAAC 48 TRIM27 5987 broad.mit.edu 36 6 28980344 28980344 + Frame_Shift_Del DEL A - A novel Unknown TCGA-24-2290-01 TCGA-24-2290-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 28980344 28980344 TRIM27 6 A - A 13