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 Tumor_Sample_UUID Matched_Norm_Sample_UUID chromosome_name_WU start_WU stop_WU reference_WU variant_WU type_WU gene_name_WU transcript_name_WU transcript_species_WU transcript_source_WU transcript_version_WU strand_WU transcript_status_WU trv_type_WU c_position_WU amino_acid_change_WU ucsc_cons_WU domain_WU all_domains_WU deletion_substructures_WU transcript_error_WU default_gene_name_WU gene_name_source_WU ensembl_gene_id normal_ref_reads normal_var_reads normal_vaf tumor_ref_reads tumors_var_reads tumor_vaf EVS_EA EVS_AA EVS_All APC 0 genome.wustl.edu 37 5 112173676 112173676 + Silent SNP C C T TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 5 112173676 112173676 C T SNP APC ENST00000257430 human ensembl 69_37n +1 known silent c.2385 p.L795 0.334 NULL pfam_APC_basic_dom,pfam_EB1-bd,pfam_APC_Cys-rich_rpt,pfam_Armadillo,pfam_SAMP,pfam_APC_15aa_rpt,superfamily_ARM-type_fold,smart_Armadillo,pfscan_Armadillo - no_errors APC HGNC ENSG00000134982 27 0 0.00 16 6 27.27 - - - BCL2L14 0 genome.wustl.edu 37 12 12232555 12232555 + Missense_Mutation SNP C C G TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 12 12232555 12232555 C G SNP BCL2L14 ENST00000308721 human ensembl 69_37n +1 known missense c.316 p.Q106E 0.001 NULL pfscan_Bcl2-like_apoptosis - no_errors BCL2L14 HGNC ENSG00000121380 34 0 0.00 18 7 28.00 - - - BRD1 0 genome.wustl.edu 37 22 50217038 50217038 + Missense_Mutation SNP C C T TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 22 50217038 50217038 C T SNP BRD1 ENST00000216267 human ensembl 69_37n -1 known missense c.928 p.E310K 1.000 superfamily_Znf_FYVE_PHD pfam_Enhancer_polycomb-like_N,pfam_Bromodomain,pfam_PWWP,superfamily_Bromodomain,superfamily_Znf_FYVE_PHD,smart_Znf_PHD,smart_Bromodomain,smart_PWWP,pfscan_PWWP,pfscan_Znf_PHD-finger,pfscan_Bromodomain,prints_Bromodomain - no_errors BRD1 HGNC ENSG00000100425 18 0 0.00 17 8 32.00 - - - BRF1 0 genome.wustl.edu 37 14 105695168 105695168 + Missense_Mutation SNP C C A TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 14 105695168 105695168 C A SNP BRF1 ENST00000546417 human ensembl 69_37n -1 putative missense c.337 p.A113S 0.036 pfam_TFIIB_cyclin,superfamily_Cyclin-like,smart_Cyclin-like pfam_TFIIB_cyclin,superfamily_Cyclin-like,smart_Cyclin-like - no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region BRF1 HGNC ENSG00000185024 83 0 0.00 46 22 32.35 - - - CDH1 0 genome.wustl.edu 37 16 68835780 68835781 + Frame_Shift_Ins INS - - C TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 - - Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 16 68835780 68835781 - C INS CDH1 ENST00000261769 human ensembl 69_37n +1 known frame_shift_ins c.371_372 p.P127fs 0.005:0.015 superfamily_Cadherin-like pfam_Cadherin,pfam_Cadherin_cytoplasmic-dom,pfam_Cadherin_pro_dom,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin - no_errors CDH1 HGNC ENSG00000039068 61 0 0.00 14 17 54.84 - - - CH25H 0 genome.wustl.edu 37 10 90966611 90966611 + Missense_Mutation SNP G G T TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 10 90966611 90966611 G T SNP CH25H ENST00000371852 human ensembl 69_37n -1 known missense c.439 p.H147N 1.000 pfam_Fatty_acid_hydroxylase pfam_Fatty_acid_hydroxylase - no_errors CH25H HGNC ENSG00000138135 49 0 0.00 21 15 41.67 - - - CHML 0 genome.wustl.edu 37 1 241798530 241798530 + Missense_Mutation SNP T T G TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 T T Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 1 241798530 241798530 T G SNP CHML ENST00000366553 human ensembl 69_37n -1 known missense c.539 p.K180T 0.075 pirsf_Rab_geranylTrfase_A_euk pfam_GDP_dissociation_inhibitor,pirsf_Rab_geranylTrfase_A_euk,prints_Rab_escort,prints_GDP_dissociation_inhibitor - no_errors CHML HGNC ENSG00000203668 184 0 0.00 152 55 26.57 - - - CREB3L4 0 genome.wustl.edu 37 1 153941846 153941846 + Missense_Mutation SNP G G A TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 1 153941846 153941846 G A SNP CREB3L4 ENST00000271889 human ensembl 69_37n +1 known missense c.458 p.C153Y 0.957 NULL pfam_bZIP_1,pfam_bZIP_2,superfamily_Euk_TF_DNA-bd,smart_bZIP,pfscan_bZIP - no_errors CREB3L4 HGNC ENSG00000143578 52 0 0.00 50 35 41.18 - - - DCAF12L1 0 genome.wustl.edu 37 X 125686114 125686114 + Missense_Mutation SNP A A C TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 A A Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf X 125686114 125686114 A C SNP DCAF12L1 ENST00000371126 human ensembl 69_37n -1 known missense c.478 p.S160A 1.000 superfamily_WD40_repeat_dom pfam_WD40_repeat,superfamily_WD40_repeat_dom,smart_WD40_repeat,pfscan_WD40_repeat,pfscan_WD40_repeat_dom - no_errors DCAF12L1 HGNC ENSG00000198889 47 0 0.00 38 23 37.70 - - - DIP2A 0 genome.wustl.edu 37 21 47978254 47978254 + Missense_Mutation SNP G G A TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 21 47978254 47978254 G A SNP DIP2A ENST00000318711 human ensembl 69_37n +1 known missense c.3920 p.R1307H 0.996 pfam_AMP-dep_Synth/Lig pfam_AMP-dep_Synth/Lig,pfam_DMAP1-bd - no_errors DIP2A HGNC ENSG00000160305 19 0 0.00 14 4 22.22 - - - DOC2B 0 genome.wustl.edu 37 17 6037 6037 + Silent SNP G G A TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 17 6037 6037 G A SNP DOC2B ENST00000343572 human ensembl 69_37n -1 known silent c.897 p.N299 0.942 pfam_C2_Ca-dep,superfamily_C2_Ca/lipid-bd_dom_CaLB pfam_C2_Ca-dep,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_C2_Ca-dep,prints_C2_dom,pfscan_C2_membr_targeting - no_errors DOC2B Clone_based_vega_gene ENSG00000262359 31 0 0.00 15 6 28.57 - - - GIT1 0 genome.wustl.edu 37 17 27903567 27903567 + Silent SNP G G A TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 17 27903567 27903567 G A SNP GIT1 ENST00000394869 human ensembl 69_37n -1 known silent c.1380 p.S460 0.995 NULL pfam_GIT1_C,pfam_GIT_SHD,pfam_ArfGAP,pfam_Ankyrin_rpt,superfamily_ArfGAP,superfamily_Ankyrin_rpt-contain_dom,smart_ArfGAP,smart_Ankyrin_rpt,smart_GIT_SHD,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_ArfGAP,prints_ArfGAP - no_errors GIT1 HGNC ENSG00000108262 35 0 0.00 27 14 34.15 - - - HOGA1 0 genome.wustl.edu 37 10 99359502 99359502 + Silent SNP G G A TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 10 99359502 99359502 G A SNP HOGA1 ENST00000370646 human ensembl 69_37n +1 known silent c.534 p.L178 1.000 pfam_Dihydrodipicolinate_synth-like,prints_Dihydrodipicolinate_synth-like pfam_Dihydrodipicolinate_synth-like,prints_Dihydrodipicolinate_synth-like - no_errors HOGA1 HGNC ENSG00000241935 36 0 0.00 28 6 17.65 - - - MYBPC3 0 genome.wustl.edu 37 11 47373015 47373015 + Missense_Mutation SNP C C T TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 11 47373015 47373015 C T SNP MYBPC3 ENST00000399249 human ensembl 69_37n -1 known missense c.67 p.A23T 0.019 pfam_Ig_I-set,smart_Ig_sub,smart_Ig_sub2 pfam_Ig_I-set,pfam_Fibronectin_type3,superfamily_Fibronectin_type3,smart_Ig_sub,smart_Ig_sub2,smart_Fibronectin_type3,pfscan_Fibronectin_type3,pfscan_Ig-like - no_errors MYBPC3 HGNC ENSG00000134571 13 0 0.00 12 4 25.00 - - - POMT2 0 genome.wustl.edu 37 14 77767528 77767528 + Missense_Mutation SNP C C T TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 14 77767528 77767528 C T SNP POMT2 ENST00000261534 human ensembl 69_37n -1 known missense c.721 p.G241R 1.000 pfam_Glyco_trans_39 pfam_Glyco_trans_39,pfam_MIR,superfamily_MIR,smart_MIR_motif,pfscan_MIR_motif - no_errors POMT2 HGNC ENSG00000009830 43 0 0.00 20 14 41.18 - - - ROS1 0 genome.wustl.edu 37 6 117642471 117642471 + Nonsense_Mutation SNP G G A TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 6 117642471 117642471 G A SNP ROS1 ENST00000368508 human ensembl 69_37n -1 known nonsense c.5728 p.R1910* 0.587 NULL pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Fibronectin_type3,pfam_Prot_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_Fibronectin_type3,smart_Fibronectin_type3,smart_LDLR_classB_rpt,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_Fibronectin_type3,pfscan_Prot_kinase_cat_dom - no_errors ROS1 HGNC ENSG00000047936 71 0 0.00 33 6 15.38 - - - RYR2 0 genome.wustl.edu 37 1 237813233 237813233 + Silent SNP C C T TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 1 237813233 237813233 C T SNP RYR2 ENST00000360064 human ensembl 69_37n +1 known silent c.7563 p.A2521 0.816 NULL pfam_Ca-rel_channel,pfam_Ryanodine_rcpt,pfam_Ryanrecept_TM4-6,pfam_SPRY_rcpt,pfam_Ins145_P3_rcpt,pfam_MIR,pfam_RIH_assoc-dom,pfam_Ion_trans_dom,superfamily_MIR,superfamily_ConA-like_lec_gl,smart_MIR_motif,smart_SPla/RYanodine_receptor_subgr,prints_Ryan_recept,pfscan_B30.2/SPRY,pfscan_EF_HAND_2,pfscan_MIR_motif - no_errors RYR2 HGNC ENSG00000198626 72 0 0.00 63 15 19.23 - - - SCGB2A1 0 genome.wustl.edu 37 11 61977888 61977888 + Missense_Mutation SNP C C G TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 11 61977888 61977888 C G SNP SCGB2A1 ENST00000244930 human ensembl 69_37n +1 known missense c.59 p.S20C 0.874 pfam_Uteroglobin-like_superfam,superfamily_Secretoglobin pfam_Uteroglobin-like_superfam,superfamily_Secretoglobin - no_errors SCGB2A1 HGNC ENSG00000124939 26 0 0.00 35 9 20.00 - - - SLC25A47 0 genome.wustl.edu 37 14 100793545 100793545 + Silent SNP C C T TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 14 100793545 100793545 C T SNP SLC25A47 ENST00000361529 human ensembl 69_37n +1 known silent c.165 p.G55 0.999 pfam_Mitochondrial_sb/sol_carrier,superfamily_Mt_carrier_dom,pfscan_Mitochondrial_sb/sol_carrier pfam_Mitochondrial_sb/sol_carrier,superfamily_Mt_carrier_dom,pfscan_Mitochondrial_sb/sol_carrier,prints_Mit_carrier - no_errors SLC25A47 HGNC ENSG00000140107 44 0 0.00 31 19 37.25 - - - TBX3 0 genome.wustl.edu 37 12 115120616 115120616 + Splice_Site SNP C C T TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 12 115120616 115120616 C T SNP TBX3 ENST00000257566 human ensembl 69_37n -1 known splice_site c.389+1 e1+1 1.000 - - - no_errors TBX3 HGNC ENSG00000135111 15 0 0.00 6 7 53.85 - - - TOP3B 0 genome.wustl.edu 37 22 22318370 22318370 + Missense_Mutation SNP G G A TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 22 22318370 22318370 G A SNP TOP3B ENST00000357179 human ensembl 69_37n -1 known missense c.1129 p.R377C 1.000 pfam_Topo_IA_cen,superfamily_Topo_IA_core_domain,smart_Topo_IA_DNA-bd pfam_Topo_IA_cen,pfam_Toprim_domain,superfamily_Topo_IA_core_domain,smart_Toprim_domain,smart_Topo_IA_2,smart_Topo_IA_DNA-bd,prints_Topo_IA - no_errors TOP3B HGNC ENSG00000100038 32 0 0.00 42 15 26.32 - - - TPM2 0 genome.wustl.edu 37 9 35685029 35685029 + RNA SNP C C A TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 9 35685029 35685029 C A SNP TPM2 ENST00000471212 human ensembl 69_37n -1 known rna NULL NULL 0.000 - - - no_errors TPM2 HGNC ENSG00000198467 32 0 0.00 15 9 37.50 - - - TTLL4 0 genome.wustl.edu 37 2 219609846 219609846 + Missense_Mutation SNP T T C TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 T T Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 2 219609846 219609846 T C SNP TTLL4 ENST00000258398 human ensembl 69_37n +1 known missense c.1676 p.I559T 0.070 NULL pfam_Tub_tyr_ligase - no_errors TTLL4 HGNC ENSG00000135912 114 0 0.00 56 33 37.08 - - - USH2A 0 genome.wustl.edu 37 1 216172264 216172264 + Missense_Mutation SNP C C T TCGA-BH-A28Q-01A-11D-A16D-09 TCGA-BH-A28Q-10A-01D-A16D-09 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx 0698379c-8f4e-460d-b7da-d3f6179dafd7 99e69ff4-d3d5-42b6-b7c2-292e502b9fcf 1 216172264 216172264 C T SNP USH2A ENST00000366943 human ensembl 69_37n -1 known missense c.6622 p.V2208I 0.392 superfamily_Fibronectin_type3,smart_Fibronectin_type3,pfscan_Fibronectin_type3 pfam_Fibronectin_type3,pfam_EGF_laminin,pfam_Laminin_G,superfamily_ConA-like_lec_gl,superfamily_Fibronectin_type3,smart_LamG-like,smart_Laminin_N,smart_EGF_laminin,smart_Fibronectin_type3,smart_Laminin_G,pfscan_EGF_laminin,pfscan_Fibronectin_type3,pfscan_Laminin_G,pfscan_Laminin_N - no_errors USH2A HGNC ENSG00000042781 112 0 0.00 78 32 28.83 - - -