From 467c80d544b06dc49705e4279ad9258758de85b0 Mon Sep 17 00:00:00 2001 From: rmadupuri Date: Tue, 15 Oct 2024 13:33:02 -0400 Subject: [PATCH] add warning for germline variants in MAF and SV files --- scripts/importer/validateData.py | 7 +++++ .../study_es_0/data_mutations_extended.maf | 22 +++++++------- tests/unit_tests_validate_data.py | 30 ++++++++++++++----- 3 files changed, 41 insertions(+), 18 deletions(-) diff --git a/scripts/importer/validateData.py b/scripts/importer/validateData.py index 446a5a70..cceb2222 100755 --- a/scripts/importer/validateData.py +++ b/scripts/importer/validateData.py @@ -2397,6 +2397,9 @@ def checkMutationStatus(self, value): if value.lower() not in ['none', 'germline', 'somatic', 'loh', 'post-transcriptional modification', 'unknown', 'wildtype'] and value != '': self.logger.warning('Mutation_Status value is not in MAF format', extra={'line_number': self.line_number, 'cause': value}) + if value.lower() == 'germline': + self.logger.warning('GERMLINE variant identified from the Mutation_Status value. If this variant is not meant for public release, please remove it.', + extra={'line_number': self.line_number, 'cause': value}) return True class ClinicalValidator(Validator): @@ -3216,6 +3219,10 @@ def checkSVstatus(sv_status): if sv_status is None: self.logger.warning('No value in SV_Status, assuming the variant is SOMATIC', extra={'line_number': self.line_number}) + elif sv_status.lower() == 'germline': + self.logger.warning('GERMLINE variant identified from the SV_Status value. If this variant is not meant for public release, please remove it.', + extra={'line_number': self.line_number, + 'cause': sv_status}) else: if not sv_status.lower() in ['somatic', 'germline']: self.logger.error('Invalid SV_Status value: possible values are [SOMATIC, GERMLINE]', diff --git a/tests/test_data/study_es_0/data_mutations_extended.maf b/tests/test_data/study_es_0/data_mutations_extended.maf index 32fc3e84..400a7d64 100644 --- a/tests/test_data/study_es_0/data_mutations_extended.maf +++ b/tests/test_data/study_es_0/data_mutations_extended.maf @@ -1,4 +1,4 @@ -#version 2.4 +#version 2.4 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 MA:FImpact MA:FIS Amino_Acid_Change MA:link.MSA MA:link.PDB MA:link.var Tumor_Sample_UUID Matched_Norm_Sample_UUID HGVSc HGVSp HGVSp_Short Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count all_effects Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation ALLELE_NUM DISTANCE SYMBOL SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT PolyPhen EXON INTRON DOMAINS GMAF AFR_MAF AMR_MAF ASN_MAF EAS_MAF EUR_MAF SAS_MAF AA_MAF EA_MAF CLIN_SIG SOMATIC PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE IMPACT PICK VARIANT_CLASS TSL HGVS_OFFSET PHENO 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 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 EVS_EA EVS_AA EVS_All cbp_driver cbp_driver_annotation cbp_driver_tiers cbp_driver_tiers_annotation Zygosity.name Zygosity.code OR11H1 genome.wustl.edu GRCh37 22 16449539 16449539 -1 Missense_Mutation SNP A A G TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 A A Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx low 1.49 V89A getma.org/?cm=msa&ty=f&p=O11H1_HUMAN&rb=1&re=154&var=V89A getma.org/?cm=var&var=hg19,22,16449539,A,G&fts=all db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 c.266T>C p.Val89Ala p.V89A ENST00000252835 1/1 0 0 OR11H1,missense_variant,p.Val89Ala,ENST00000252835,NM_001005239.1; G ENSG00000130538 ENST00000252835 Transcript missense_variant 267/982 266/981 89/326 V/A gTc/gCc rs199856986,COSM1484040 1 OR11H1 HGNC 15404 protein_coding YES CCDS33594.1 ENSP00000252835 O11H1_HUMAN UPI000004B1CF NM_001005239.1 deleterious(0.02) possibly_damaging(0.589) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24242:SF201,hmmpanther:PTHR24242,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 22 16449539 16449539 A G SNP OR11H1 ENST00000252835 human ensembl 69_37n -1 known missense c.266 p.V89A 234 pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_Olfact_rcpt,prints_7TM_GPCR_Rhodpsn - no_errors OR11H1 HGNC ENSG00000130538 65 0 0 38 6 13.64 - - - 22 16449539 16449539 A G SNP OR11H1 ENST00000252835 human ensembl 69_37n -1 known missense c.266 p.V89A 234 pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_Olfact_rcpt,prints_7TM_GPCR_Rhodpsn - no_errors OR11H1 HGNC - - - Putative_Driver Test driver TMEM247 genome.wustl.edu GRCh37 2 46707888 46707888 1 Frame_Shift_Del DEL G G - TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 c.463delG p.Ala155ArgfsTer59 p.A155Rfs*59 ENST00000434431 2/3 0 0 TMEM247,frameshift_variant,p.Ala155ArgfsTer59,ENST00000434431,NM_001145051.2;TMEM247,intron_variant,,ENST00000432241,; - ENSG00000187600 ENST00000434431 Transcript frameshift_variant 462/659 462/659 154/219 E/X gaG/ga COSM1408208,~rs70940616 1 TMEM247 HGNC 42967 protein_coding YES CCDS56117.1 ENSP00000388684 TM247_HUMAN UPI0000366EF8 NM_001145051.2 2/3 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF15444 -:0.0202 -:0.0439 1 HIGH 1 deletion 1 1 2 46707888 46707888 G - DEL TMEM247 ENST00000434431 human ensembl 69_37n 1 known frame_shift_del c.462 p.A155fs 83 - no_stop_codon:bad_bp_length_for_coding_region TMEM247 HGNC ENSG00000187600 20 0 0 7 3 30 - - - 2 46707888 46707888 G - DEL TMEM247 ENST00000434431 human ensembl 69_37n 1 known frame_shift_del c.462 p.A155fs 83 - no_stop_codon:bad_bp_length_for_coding_region TMEM247 HGNC - - - Putative_Passenger Test passenger Class 2 Class annotation @@ -10,29 +10,29 @@ KAT2A genome.wustl.edu GRCh37 17 40272381 40272381 -1 Silent SNP G G A TCGA-A MSH3 genome.wustl.edu GRCh37 5 80024722 80024722 1 Frame_Shift_Del DEL T T - TCGA-A1-A0SB-02 TCGA-A1-A0SB-10 T T Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 c.1508delT p.Leu503TrpfsTer5 p.L503Wfs*5 ENST00000265081 10/24 0 0 MSH3,frameshift_variant,p.Leu503TrpfsTer5,ENST00000265081,NM_002439.4;MSH3,non_coding_transcript_exon_variant,,ENST00000512258,; - ENSG00000113318 ENST00000265081 Transcript frameshift_variant 1586/4092 1506/3414 502/1137 S/X tcT/tc 1 MSH3 HGNC 7326 protein_coding YES CCDS34195.1 ENSP00000265081 MSH3_HUMAN UPI0000DBEE85 NM_002439.4 10/24 Superfamily_domains:SSF53150,Gene3D:3.30.420.110,Pfam_domain:PF05188,hmmpanther:PTHR11361,hmmpanther:PTHR11361:SF34 HIGH 1 deletion 2 5 80024722 80024722 T - DEL MSH3 ENST00000265081 human ensembl 69_37n 1 known frame_shift_del c.1506 p.L503fs 998 pfam_DNA_mismatch_repair_MutS_connt,superfamily_DNA_mismatch_repair_MutS_connt pfam_DNA_mismatch_repair_MutS_C,pfam_DNA_mismatch_repair_MutS_core,pfam_DNA_mismatch_repair_MutS_connt,pfam_DNA_mismatch_repair_MutS-lik_N,pfam_DNA_mismatch_repair_MutS_clamp,superfamily_DNA_mismatch_repair_MutS_core,superfamily_DNA_mismatch_repair_MutS_N,superfamily_DNA_mismatch_repair_MutS_connt,smart_DNA_mismatch_repair_MutS_core,smart_DNA_mismatch_repair_MutS_C - no_errors MSH3 HGNC ENSG00000113318 83 0 0 12 2 14.29 - - - 5 80024722 80024722 T - DEL MSH3 ENST00000265081 human ensembl 69_37n 1 known frame_shift_del c.1506 p.L503fs 998 pfam_DNA_mismatch_repair_MutS_connt,superfamily_DNA_mismatch_repair_MutS_connt pfam_DNA_mismatch_repair_MutS_C,pfam_DNA_mismatch_repair_MutS_core,pfam_DNA_mismatch_repair_MutS_connt,pfam_DNA_mismatch_repair_MutS-lik_N,pfam_DNA_mismatch_repair_MutS_clamp,superfamily_DNA_mismatch_repair_MutS_core,superfamily_DNA_mismatch_repair_MutS_N,superfamily_DNA_mismatch_repair_MutS_connt,smart_DNA_mismatch_repair_MutS_core,smart_DNA_mismatch_repair_MutS_C - no_errors MSH3 HGNC - - - Putative_Passenger Test passenger Class 3 Class annotation MYB genome.wustl.edu GRCh37 6 135507043 135507044 1 Frame_Shift_Ins INS - - A TCGA-A1-A0SB-02 TCGA-A1-A0SB-10 - - Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 c.27dupA p.Tyr10IlefsTer2 p.Y10Ifs*2 ENST00000367814 2/15 0 0 MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000341911,NM_001130173.1,NM_001161658.1,NM_001161656.1;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000316528,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000442647,NM_001161660.1,NM_001130172.1;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000367814,NM_001161659.1,NM_005375.2;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000525369,NM_001161657.1;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000527615,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000528774,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000534121,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000533624,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000534044,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000420123,;MYB,upstream_gene_variant,,ENST00000430686,;MYB,non_coding_transcript_exon_variant,,ENST00000531845,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000367812,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000533837,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000438901,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000525477,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000463282,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000339290,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000533808,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000525514,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000529586,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000526889,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000526320,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000531519,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000533384,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000531737,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000529262,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000526565,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000528015,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000526187,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000525002,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000528343,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000528140,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000528345,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000525940,;MYB,frameshift_variant,p.Tyr10Ter,ENST00000531634,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000524588,; A ENSG00000118513 ENST00000367814 Transcript frameshift_variant 212-213/3302 26-27/1923 9/640 I/IX ata/atAa COSM1487247,COSM1487248 1 MYB HGNC 7545 protein_coding CCDS5174.1 ENSP00000356788 MYB_HUMAN Q9UMI7_HUMAN,Q708J0_HUMAN,Q708E9_HUMAN,Q708E3_HUMAN UPI000012FAEA NM_001161659.1,NM_005375.2 2/15 hmmpanther:PTHR10641,hmmpanther:PTHR10641:SF454 1,1 HIGH insertion 1 1,1 6 135507043 135507044 - A INS MYB ENST00000341911 human ensembl 69_37n 1 known frame_shift_ins c.26_27 p.Y10fs 1.000:0.997 pfam_C-myb_C,pfam_SANT/Myb,pfam_Tscrpt_reg_Wos2-domain,superfamily_Homeodomain-like,smart_SANT/Myb,pfscan_Myb-like_dom - no_errors MYB HGNC ENSG00000118513 50 0 0 36 4 10 - - - 6 135507043 135507044 - A INS MYB ENST00000341911 human ensembl 69_37n 1 known frame_shift_ins c.26_27 p.Y10fs 1.000:0.997 pfam_C-myb_C,pfam_SANT/Myb,pfam_Tscrpt_reg_Wos2-domain,superfamily_Homeodomain-like,smart_SANT/Myb,pfscan_Myb-like_dom - no_errors MYB HGNC - - - Putative_Passenger Test passenger PIEZO1 genome.wustl.edu GRCh37 16 88790292 88790292 -1 Missense_Mutation SNP T T C TCGA-A1-A0SB-02 TCGA-A1-A0SB-10 T T Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx low 1.18 Q1441R getma.org/?cm=msa&ty=f&p=PIEZ1_HUMAN&rb=58&re=1627&var=Q1441R getma.org/?cm=var&var=hg19,16,88790292,T,C&fts=all db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 c.4322A>G p.Gln1441Arg p.Q1441R ENST00000301015 31/51 0 0 PIEZO1,missense_variant,p.Gln1441Arg,ENST00000301015,NM_001142864.2;PIEZO1,missense_variant,p.Gln115Arg,ENST00000474606,;PIEZO1,upstream_gene_variant,,ENST00000327397,;PIEZO1,upstream_gene_variant,,ENST00000466823,;RP5-1142A6.9,downstream_gene_variant,,ENST00000564984,;PIEZO1,non_coding_transcript_exon_variant,,ENST00000566414,;PIEZO1,upstream_gene_variant,,ENST00000419505,;PIEZO1,upstream_gene_variant,,ENST00000497793,;PIEZO1,upstream_gene_variant,,ENST00000495568,;PIEZO1,downstream_gene_variant,,ENST00000475586,;PIEZO1,downstream_gene_variant,,ENST00000491917,; C ENSG00000103335 ENST00000301015 Transcript missense_variant 4569/8072 4322/7566 1441/2521 Q/R cAg/cGg COSM1479166 1 PIEZO1 HGNC 28993 protein_coding YES CCDS54058.1 ENSP00000301015 PIEZ1_HUMAN UPI0001B300F3 NM_001142864.2 tolerated(0.25) possibly_damaging(0.78) 31/51 hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF40 1 MODERATE 1 SNV 1 16 88790292 88790292 T C SNP PIEZO1 ENST00000301015 human ensembl 69_37n -1 novel missense c.4322 p.Q1441R 1000 pfam_DUF3595 - no_errors PIEZO1 HGNC ENSG00000103335 37 0 0 20 8 28.57 - - - 16 88790292 88790292 T C SNP PIEZO1 ENST00000301015 human ensembl 69_37n -1 novel missense c.4322 p.Q1441R 1000 pfam_DUF3595 - no_errors PIEZO1 HGNC - - - Putative_Passenger Test passenger Class 3 Class annotation -TP53 genome.wustl.edu GRCh37 17 7578253 7578253 0 Missense_Mutation SNP C C A TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 A C Unknown Germline Phase_IV Capture 1 dbGAP IlluminaGAIIx medium 3.005 getma.org/?cm=msa&ty=f&p=P53_HUMAN&rb=95&re=289&var=G199V getma.org/pdb.php?prot=P53_HUMAN&from=95&to=289&var=G199V getma.org/?cm=var&var=hg19,17,7578253,C,A&fts=all ENST00000269305.4:c.596G>T p.Gly199Val p.G199V ENST00000269305 11-Jun 0 0 TP53,missense_variant,p.Gly199Val,ENST00000420246,NM_001126114.2,NM_001276696.1;TP53,missense_variant,p.Gly199Val,ENST00000455263,NM_001276695.1,NM_001126113.2;TP53,missense_variant,p.Gly199Val,ENST00000269305,NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1;TP53,missense_variant,p.Gly199Val,ENST00000445888,;TP53,missense_variant,p.Gly199Val,ENST00000359597,;TP53,missense_variant,p.Gly199Val,ENST00000413465,;TP53,missense_variant,p.Gly67Val,ENST00000509690,;TP53,missense_variant,p.Gly106Val,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,intron_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; A ENSG00000141510 ENST00000269305 Transcript missense_variant 786/2579 596/1182 199 G/V gGa/gTa TP53_g.12665G>T,COSM44140,COSM255788,COSM255787,COSM255789,COSM3675525,COSM3675524,COSM255790 1 TP53 HGNC 11998 protein_coding YES CCDS11118.1 ENSP00000269305 P53_HUMAN S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN UPI000002ED67 NM_001126112.2 deleterious(0) probably_damaging(1) 11-Jun Gene3D:2.60.40.720,Pfam_domain:PF00870,hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Superfamily_domains:SSF49417 0,1,1,1,1,1,1,1 MODERATE 1 SNV 0,1,1,1,1,1,1,1 17 7578253 7578253 C A SNP TP53 NM_000546.4 human genbank 58_37c -1 reviewed missense c.596 p.G199V 1 HMMPfam_P53|7Csuperfamily_p53-like transcription factors HMMPfam_P53_TAD|7CHMMPfam_P53|7Csuperfamily_p53-like transcription factors|7CPatternScan_P53|7CHMMPfam_P53_tetramer|7Csuperfamily_p53 tetramerization domain - 17 7578253 7578253 C A SNP TP53 NM_000546.4 human genbank 58_37c -1 reviewed missense c.596 p.G199V 1 HMMPfam_P53|7Csuperfamily_p53-like transcription factors HMMPfam_P53_TAD|7CHMMPfam_P53|7Csuperfamily_p53-like transcription factors|7CPatternScan_P53|7CHMMPfam_P53_tetramer|7Csuperfamily_p53 tetramerization domain - +TP53 genome.wustl.edu GRCh37 17 7578253 7578253 0 Missense_Mutation SNP C C A TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 A C Unknown Somatic Phase_IV Capture 1 dbGAP IlluminaGAIIx medium 3.005 getma.org/?cm=msa&ty=f&p=P53_HUMAN&rb=95&re=289&var=G199V getma.org/pdb.php?prot=P53_HUMAN&from=95&to=289&var=G199V getma.org/?cm=var&var=hg19,17,7578253,C,A&fts=all ENST00000269305.4:c.596G>T p.Gly199Val p.G199V ENST00000269305 11-Jun 0 0 TP53,missense_variant,p.Gly199Val,ENST00000420246,NM_001126114.2,NM_001276696.1;TP53,missense_variant,p.Gly199Val,ENST00000455263,NM_001276695.1,NM_001126113.2;TP53,missense_variant,p.Gly199Val,ENST00000269305,NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1;TP53,missense_variant,p.Gly199Val,ENST00000445888,;TP53,missense_variant,p.Gly199Val,ENST00000359597,;TP53,missense_variant,p.Gly199Val,ENST00000413465,;TP53,missense_variant,p.Gly67Val,ENST00000509690,;TP53,missense_variant,p.Gly106Val,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,intron_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; A ENSG00000141510 ENST00000269305 Transcript missense_variant 786/2579 596/1182 199 G/V gGa/gTa TP53_g.12665G>T,COSM44140,COSM255788,COSM255787,COSM255789,COSM3675525,COSM3675524,COSM255790 1 TP53 HGNC 11998 protein_coding YES CCDS11118.1 ENSP00000269305 P53_HUMAN S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN UPI000002ED67 NM_001126112.2 deleterious(0) probably_damaging(1) 11-Jun Gene3D:2.60.40.720,Pfam_domain:PF00870,hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Superfamily_domains:SSF49417 0,1,1,1,1,1,1,1 MODERATE 1 SNV 0,1,1,1,1,1,1,1 17 7578253 7578253 C A SNP TP53 NM_000546.4 human genbank 58_37c -1 reviewed missense c.596 p.G199V 1 HMMPfam_P53|7Csuperfamily_p53-like transcription factors HMMPfam_P53_TAD|7CHMMPfam_P53|7Csuperfamily_p53-like transcription factors|7CPatternScan_P53|7CHMMPfam_P53_tetramer|7Csuperfamily_p53 tetramerization domain - 17 7578253 7578253 C A SNP TP53 NM_000546.4 human genbank 58_37c -1 reviewed missense c.596 p.G199V 1 HMMPfam_P53|7Csuperfamily_p53-like transcription factors HMMPfam_P53_TAD|7CHMMPfam_P53|7Csuperfamily_p53-like transcription factors|7CPatternScan_P53|7CHMMPfam_P53_tetramer|7Csuperfamily_p53 tetramerization domain - TP53 genome.wustl.edu GRCh37 17 7576851 7576851 0 Splice_Site SNP A A C novel unknown TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 A A Unknown Somatic Phase_IV Capture 1 dbGAP Illumina GAIIx ENST00000269305.4:c.993+2T>G p.X331_splice ENST00000269305 0 0 TP53,splice_donor_variant,,ENST00000420246,NM_001126114.2,NM_001276696.1;TP53,splice_donor_variant,,ENST00000455263,NM_001276695.1,NM_001126113.2;TP53,splice_donor_variant,,ENST00000269305,NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1;TP53,splice_donor_variant,,ENST00000445888,;TP53,splice_donor_variant,,ENST00000359597,;TP53,splice_donor_variant,,ENST00000576024,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000509690,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,splice_donor_variant,,ENST00000510385,;TP53,splice_donor_variant,,ENST00000504290,;TP53,splice_donor_variant,,ENST00000504937,;TP53,downstream_gene_variant,,ENST00000505014,; C ENSG00000141510 ENST00000269305 Transcript splice_donor_variant -/2579 993/1182 TP53_g.14067T>G,COSM29774,COSM146229 1 TP53 HGNC 11998 protein_coding YES CCDS11118.1 ENSP00000269305 P53_HUMAN S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN UPI000002ED67 NM_001126112.2 10-Sep 0,1,1 HIGH 1 SNV 0,1,1 17 7576851 7576851 A C SNP TP53 NM_000546 human genbank 57_37b -1 reviewed splice_site c.993+2 e8+2 1 - - - 17 7576851 7576851 A C SNP TP53 NM_000546 human genbank 57_37b -1 reviewed splice_site c.993+2 e8+2 1 - - - -BRCA1 genome.wustl.edu GRCh37 17 41243581 41243581 0 Nonsense_Mutation SNP G G A rs80357262 TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 A G Unknown Germline Phase_IV Capture 1 dbGAP IlluminaGAIIx 0 getma.org/?cm=var&var=hg19,17,41243581,G,A&fts=all ENST00000357654.3:c.3967C>T p.Gln1323Ter p.Q1323* ENST00000357654 23-Oct 0 0 BRCA1,stop_gained,p.Gln1027Ter,ENST00000309486,NM_007297.3;BRCA1,stop_gained,p.Gln1323Ter,ENST00000357654,NM_007294.3;BRCA1,stop_gained,p.Gln1323Ter,ENST00000346315,;BRCA1,stop_gained,p.Gln1323Ter,ENST00000354071,;BRCA1,stop_gained,p.Gln1323Ter,ENST00000471181,NM_007300.3;BRCA1,stop_gained,p.Gln1276Ter,ENST00000493795,;BRCA1,stop_gained,p.Gln88Ter,ENST00000461574,;BRCA1,intron_variant,,ENST00000352993,;BRCA1,intron_variant,,ENST00000351666,;BRCA1,intron_variant,,ENST00000468300,NM_007299.3;BRCA1,intron_variant,,ENST00000491747,NM_007298.3;BRCA1,intron_variant,,ENST00000478531,;BRCA1,intron_variant,,ENST00000493919,;BRCA1,intron_variant,,ENST00000484087,;BRCA1,intron_variant,,ENST00000591534,;BRCA1,intron_variant,,ENST00000487825,;BRCA1,intron_variant,,ENST00000586385,;BRCA1,intron_variant,,ENST00000591849,;BRCA1,downstream_gene_variant,,ENST00000470026,;BRCA1,downstream_gene_variant,,ENST00000477152,;BRCA1,downstream_gene_variant,,ENST00000494123,;BRCA1,downstream_gene_variant,,ENST00000473961,;BRCA1,downstream_gene_variant,,ENST00000497488,;BRCA1,downstream_gene_variant,,ENST00000476777,;BRCA1,3_prime_UTR_variant,,ENST00000461221,;BRCA1,non_coding_transcript_exon_variant,,ENST00000467274,;BRCA1,downstream_gene_variant,,ENST00000492859,;BRCA1,downstream_gene_variant,,ENST00000412061,; A ENSG00000012048 ENST00000357654 Transcript stop_gained 4086/7094 3967/5592 1323 Q/* Caa/Taa rs80357262 1 BRCA1 HGNC 1100 protein_coding CCDS11453.1 ENSP00000350283 BRCA1_HUMAN Q9UE29_HUMAN,Q9NQR3_HUMAN,Q92897_HUMAN,Q7KYU6_HUMAN,Q4EW25_HUMAN,Q3YB53_HUMAN,Q3YB50_HUMAN,Q3YB49_HUMAN,Q3LRH8_HUMAN,Q3B891_HUMAN,K7EPC7_HUMAN,K4K7V3_HUMAN,K4JXS7_HUMAN,K4JUB1_HUMAN,G4V503_HUMAN,G4V502_HUMAN,G4V500_HUMAN,G4V4Z8_HUMAN,G4V4Z7_HUMAN,G1UI37_HUMAN,E9PFZ0_HUMAN,E7EWN5_HUMAN,E7EP70_HUMAN,C9IZW4_HUMAN,C4PFY7_HUMAN UPI0000126AC8 NM_007294.3 23-Oct PIRSF_domain:PIRSF001734,hmmpanther:PTHR13763,hmmpanther:PTHR13763:SF0 not_provided,pathogenic HIGH SNV 1 17 41243581 41243581 G A SNP BRCA1 NM_007294.3 human genbank 58_37c -1 reviewed nonsense c.3967 p.Q1323* 0.949 HMMPfam_BRCT|7CHMMSmart_SM00292|7Csuperfamily_BRCT domain|7CHMMSmart_SM00184|7CPatternScan_ZF_RING_1|7CHMMPfam_zf-C3HC4|7Csuperfamily_RING/U-box - 17 41243581 41243581 G A SNP BRCA1 NM_007294.3 human genbank 58_37c -1 reviewed nonsense c.3967 p.Q1323* 0.949 HMMPfam_BRCT|7CHMMSmart_SM00292|7Csuperfamily_BRCT domain|7CHMMSmart_SM00184|7CPatternScan_ZF_RING_1|7CHMMPfam_zf-C3HC4|7Csuperfamily_RING/U-box - +BRCA1 genome.wustl.edu GRCh37 17 41243581 41243581 0 Nonsense_Mutation SNP G G A rs80357262 TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 A G Unknown Somatic Phase_IV Capture 1 dbGAP IlluminaGAIIx 0 getma.org/?cm=var&var=hg19,17,41243581,G,A&fts=all ENST00000357654.3:c.3967C>T p.Gln1323Ter p.Q1323* ENST00000357654 23-Oct 0 0 BRCA1,stop_gained,p.Gln1027Ter,ENST00000309486,NM_007297.3;BRCA1,stop_gained,p.Gln1323Ter,ENST00000357654,NM_007294.3;BRCA1,stop_gained,p.Gln1323Ter,ENST00000346315,;BRCA1,stop_gained,p.Gln1323Ter,ENST00000354071,;BRCA1,stop_gained,p.Gln1323Ter,ENST00000471181,NM_007300.3;BRCA1,stop_gained,p.Gln1276Ter,ENST00000493795,;BRCA1,stop_gained,p.Gln88Ter,ENST00000461574,;BRCA1,intron_variant,,ENST00000352993,;BRCA1,intron_variant,,ENST00000351666,;BRCA1,intron_variant,,ENST00000468300,NM_007299.3;BRCA1,intron_variant,,ENST00000491747,NM_007298.3;BRCA1,intron_variant,,ENST00000478531,;BRCA1,intron_variant,,ENST00000493919,;BRCA1,intron_variant,,ENST00000484087,;BRCA1,intron_variant,,ENST00000591534,;BRCA1,intron_variant,,ENST00000487825,;BRCA1,intron_variant,,ENST00000586385,;BRCA1,intron_variant,,ENST00000591849,;BRCA1,downstream_gene_variant,,ENST00000470026,;BRCA1,downstream_gene_variant,,ENST00000477152,;BRCA1,downstream_gene_variant,,ENST00000494123,;BRCA1,downstream_gene_variant,,ENST00000473961,;BRCA1,downstream_gene_variant,,ENST00000497488,;BRCA1,downstream_gene_variant,,ENST00000476777,;BRCA1,3_prime_UTR_variant,,ENST00000461221,;BRCA1,non_coding_transcript_exon_variant,,ENST00000467274,;BRCA1,downstream_gene_variant,,ENST00000492859,;BRCA1,downstream_gene_variant,,ENST00000412061,; A ENSG00000012048 ENST00000357654 Transcript stop_gained 4086/7094 3967/5592 1323 Q/* Caa/Taa rs80357262 1 BRCA1 HGNC 1100 protein_coding CCDS11453.1 ENSP00000350283 BRCA1_HUMAN Q9UE29_HUMAN,Q9NQR3_HUMAN,Q92897_HUMAN,Q7KYU6_HUMAN,Q4EW25_HUMAN,Q3YB53_HUMAN,Q3YB50_HUMAN,Q3YB49_HUMAN,Q3LRH8_HUMAN,Q3B891_HUMAN,K7EPC7_HUMAN,K4K7V3_HUMAN,K4JXS7_HUMAN,K4JUB1_HUMAN,G4V503_HUMAN,G4V502_HUMAN,G4V500_HUMAN,G4V4Z8_HUMAN,G4V4Z7_HUMAN,G1UI37_HUMAN,E9PFZ0_HUMAN,E7EWN5_HUMAN,E7EP70_HUMAN,C9IZW4_HUMAN,C4PFY7_HUMAN UPI0000126AC8 NM_007294.3 23-Oct PIRSF_domain:PIRSF001734,hmmpanther:PTHR13763,hmmpanther:PTHR13763:SF0 not_provided,pathogenic HIGH SNV 1 17 41243581 41243581 G A SNP BRCA1 NM_007294.3 human genbank 58_37c -1 reviewed nonsense c.3967 p.Q1323* 0.949 HMMPfam_BRCT|7CHMMSmart_SM00292|7Csuperfamily_BRCT domain|7CHMMSmart_SM00184|7CPatternScan_ZF_RING_1|7CHMMPfam_zf-C3HC4|7Csuperfamily_RING/U-box - 17 41243581 41243581 G A SNP BRCA1 NM_007294.3 human genbank 58_37c -1 reviewed nonsense c.3967 p.Q1323* 0.949 HMMPfam_BRCT|7CHMMSmart_SM00292|7Csuperfamily_BRCT domain|7CHMMSmart_SM00184|7CPatternScan_ZF_RING_1|7CHMMPfam_zf-C3HC4|7Csuperfamily_RING/U-box - BRCA1 genome.wustl.edu GRCh37 17 41243581 41243581 0 Missense_Mutation SNP G G A rs80357262 TEST_SAMPLE_SOMATIC_HOMOZYGOUS TCGA-A1-A0SB-10 A G Unknown Somatic Phase_IV Capture 1 dbGAP IlluminaGAIIx 0 getma.org/?cm=var&var=hg19,17,41243581,G,A&fts=all ENST00000357654.3:c.3967C>T p.Ser1436Ser p.S1436S ENST00000357654 23-Oct 0 0 BRCA1,stop_gained,p.Gln1027Ter,ENST00000309486,NM_007297.3;BRCA1,stop_gained,p.Gln1323Ter,ENST00000357654,NM_007294.3;BRCA1,stop_gained,p.Gln1323Ter,ENST00000346315,;BRCA1,stop_gained,p.Gln1323Ter,ENST00000354071,;BRCA1,stop_gained,p.Gln1323Ter,ENST00000471181,NM_007300.3;BRCA1,stop_gained,p.Gln1276Ter,ENST00000493795,;BRCA1,stop_gained,p.Gln88Ter,ENST00000461574,;BRCA1,intron_variant,,ENST00000352993,;BRCA1,intron_variant,,ENST00000351666,;BRCA1,intron_variant,,ENST00000468300,NM_007299.3;BRCA1,intron_variant,,ENST00000491747,NM_007298.3;BRCA1,intron_variant,,ENST00000478531,;BRCA1,intron_variant,,ENST00000493919,;BRCA1,intron_variant,,ENST00000484087,;BRCA1,intron_variant,,ENST00000591534,;BRCA1,intron_variant,,ENST00000487825,;BRCA1,intron_variant,,ENST00000586385,;BRCA1,intron_variant,,ENST00000591849,;BRCA1,downstream_gene_variant,,ENST00000470026,;BRCA1,downstream_gene_variant,,ENST00000477152,;BRCA1,downstream_gene_variant,,ENST00000494123,;BRCA1,downstream_gene_variant,,ENST00000473961,;BRCA1,downstream_gene_variant,,ENST00000497488,;BRCA1,downstream_gene_variant,,ENST00000476777,;BRCA1,3_prime_UTR_variant,,ENST00000461221,;BRCA1,non_coding_transcript_exon_variant,,ENST00000467274,;BRCA1,downstream_gene_variant,,ENST00000492859,;BRCA1,downstream_gene_variant,,ENST00000412061,; A ENSG00000012048 ENST00000357654 Transcript stop_gained 4086/7094 3967/5592 1323 Q/* Caa/Taa rs80357262 1 BRCA1 HGNC 1100 protein_coding CCDS11453.1 ENSP00000350283 BRCA1_HUMAN Q9UE29_HUMAN,Q9NQR3_HUMAN,Q92897_HUMAN,Q7KYU6_HUMAN,Q4EW25_HUMAN,Q3YB53_HUMAN,Q3YB50_HUMAN,Q3YB49_HUMAN,Q3LRH8_HUMAN,Q3B891_HUMAN,K7EPC7_HUMAN,K4K7V3_HUMAN,K4JXS7_HUMAN,K4JUB1_HUMAN,G4V503_HUMAN,G4V502_HUMAN,G4V500_HUMAN,G4V4Z8_HUMAN,G4V4Z7_HUMAN,G1UI37_HUMAN,E9PFZ0_HUMAN,E7EWN5_HUMAN,E7EP70_HUMAN,C9IZW4_HUMAN,C4PFY7_HUMAN UPI0000126AC8 NM_007294.3 23-Oct PIRSF_domain:PIRSF001734,hmmpanther:PTHR13763,hmmpanther:PTHR13763:SF0 not_provided,pathogenic HIGH SNV 1 17 41243581 41243581 G A SNP BRCA1 NM_007294.3 human genbank 58_37c -1 reviewed nonsense c.3967 p.Q1323* 0.949 HMMPfam_BRCT|7CHMMSmart_SM00292|7Csuperfamily_BRCT domain|7CHMMSmart_SM00184|7CPatternScan_ZF_RING_1|7CHMMPfam_zf-C3HC4|7Csuperfamily_RING/U-box - 17 41243581 41243581 G A SNP BRCA1 NM_007294.3 human genbank 58_37c -1 reviewed nonsense c.3967 p.Q1323* 0.949 HMMPfam_BRCT|7CHMMSmart_SM00292|7Csuperfamily_BRCT domain|7CHMMSmart_SM00184|7CPatternScan_ZF_RING_1|7CHMMPfam_zf-C3HC4|7Csuperfamily_RING/U-box - Putative_Driver Test driver Class 1 Class annotation Homozygous 2 BRCA1 genome.wustl.edu GRCh37 17 41243581 41243581 0 Missense_Mutation SNP G G A rs80357262 TEST_SAMPLE_SOMATIC_HETEROZYGOUS TCGA-A1-A0SB-10 A G Unknown Somatic Phase_IV Capture 1 dbGAP IlluminaGAIIx 0 getma.org/?cm=var&var=hg19,17,41243581,G,A&fts=all ENST00000357654.3:c.3967C>T p.Ser694Ser p.S694S ENST00000357654 23-Oct 0 0 BRCA1,stop_gained,p.Gln1027Ter,ENST00000309486,NM_007297.3;BRCA1,stop_gained,p.Gln1323Ter,ENST00000357654,NM_007294.3;BRCA1,stop_gained,p.Gln1323Ter,ENST00000346315,;BRCA1,stop_gained,p.Gln1323Ter,ENST00000354071,;BRCA1,stop_gained,p.Gln1323Ter,ENST00000471181,NM_007300.3;BRCA1,stop_gained,p.Gln1276Ter,ENST00000493795,;BRCA1,stop_gained,p.Gln88Ter,ENST00000461574,;BRCA1,intron_variant,,ENST00000352993,;BRCA1,intron_variant,,ENST00000351666,;BRCA1,intron_variant,,ENST00000468300,NM_007299.3;BRCA1,intron_variant,,ENST00000491747,NM_007298.3;BRCA1,intron_variant,,ENST00000478531,;BRCA1,intron_variant,,ENST00000493919,;BRCA1,intron_variant,,ENST00000484087,;BRCA1,intron_variant,,ENST00000591534,;BRCA1,intron_variant,,ENST00000487825,;BRCA1,intron_variant,,ENST00000586385,;BRCA1,intron_variant,,ENST00000591849,;BRCA1,downstream_gene_variant,,ENST00000470026,;BRCA1,downstream_gene_variant,,ENST00000477152,;BRCA1,downstream_gene_variant,,ENST00000494123,;BRCA1,downstream_gene_variant,,ENST00000473961,;BRCA1,downstream_gene_variant,,ENST00000497488,;BRCA1,downstream_gene_variant,,ENST00000476777,;BRCA1,3_prime_UTR_variant,,ENST00000461221,;BRCA1,non_coding_transcript_exon_variant,,ENST00000467274,;BRCA1,downstream_gene_variant,,ENST00000492859,;BRCA1,downstream_gene_variant,,ENST00000412061,; A ENSG00000012048 ENST00000357654 Transcript stop_gained 4086/7094 3967/5592 1323 Q/* Caa/Taa rs80357262 1 BRCA1 HGNC 1100 protein_coding CCDS11453.1 ENSP00000350283 BRCA1_HUMAN Q9UE29_HUMAN,Q9NQR3_HUMAN,Q92897_HUMAN,Q7KYU6_HUMAN,Q4EW25_HUMAN,Q3YB53_HUMAN,Q3YB50_HUMAN,Q3YB49_HUMAN,Q3LRH8_HUMAN,Q3B891_HUMAN,K7EPC7_HUMAN,K4K7V3_HUMAN,K4JXS7_HUMAN,K4JUB1_HUMAN,G4V503_HUMAN,G4V502_HUMAN,G4V500_HUMAN,G4V4Z8_HUMAN,G4V4Z7_HUMAN,G1UI37_HUMAN,E9PFZ0_HUMAN,E7EWN5_HUMAN,E7EP70_HUMAN,C9IZW4_HUMAN,C4PFY7_HUMAN UPI0000126AC8 NM_007294.3 23-Oct PIRSF_domain:PIRSF001734,hmmpanther:PTHR13763,hmmpanther:PTHR13763:SF0 not_provided,pathogenic HIGH SNV 1 17 41243581 41243581 G A SNP BRCA1 NM_007294.3 human genbank 58_37c -1 reviewed nonsense c.3967 p.Q1323* 0.949 HMMPfam_BRCT|7CHMMSmart_SM00292|7Csuperfamily_BRCT domain|7CHMMSmart_SM00184|7CPatternScan_ZF_RING_1|7CHMMPfam_zf-C3HC4|7Csuperfamily_RING/U-box - 17 41243581 41243581 G A SNP BRCA1 NM_007294.3 human genbank 58_37c -1 reviewed nonsense c.3967 p.Q1323* 0.949 HMMPfam_BRCT|7CHMMSmart_SM00292|7Csuperfamily_BRCT domain|7CHMMSmart_SM00184|7CPatternScan_ZF_RING_1|7CHMMPfam_zf-C3HC4|7Csuperfamily_RING/U-box - Putative_Passenger Test passenger Class 1 Class annotation Heterozygous 1 BRCA1 genome.wustl.edu GRCh37 17 41243581 41243581 0 Missense_Mutation SNP G G A rs80357262 TEST_SAMPLE_SOMATIC_UNDEFINED TCGA-A1-A0SB-10 A G Unknown Somatic Phase_IV Capture 1 dbGAP IlluminaGAIIx 0 getma.org/?cm=var&var=hg19,17,41243581,G,A&fts=all ENST00000357654.3:c.3967C>T p.Pro871Gln p.P871Q ENST00000357654 23-Oct 0 0 BRCA1,stop_gained,p.Gln1027Ter,ENST00000309486,NM_007297.3;BRCA1,stop_gained,p.Gln1323Ter,ENST00000357654,NM_007294.3;BRCA1,stop_gained,p.Gln1323Ter,ENST00000346315,;BRCA1,stop_gained,p.Gln1323Ter,ENST00000354071,;BRCA1,stop_gained,p.Gln1323Ter,ENST00000471181,NM_007300.3;BRCA1,stop_gained,p.Gln1276Ter,ENST00000493795,;BRCA1,stop_gained,p.Gln88Ter,ENST00000461574,;BRCA1,intron_variant,,ENST00000352993,;BRCA1,intron_variant,,ENST00000351666,;BRCA1,intron_variant,,ENST00000468300,NM_007299.3;BRCA1,intron_variant,,ENST00000491747,NM_007298.3;BRCA1,intron_variant,,ENST00000478531,;BRCA1,intron_variant,,ENST00000493919,;BRCA1,intron_variant,,ENST00000484087,;BRCA1,intron_variant,,ENST00000591534,;BRCA1,intron_variant,,ENST00000487825,;BRCA1,intron_variant,,ENST00000586385,;BRCA1,intron_variant,,ENST00000591849,;BRCA1,downstream_gene_variant,,ENST00000470026,;BRCA1,downstream_gene_variant,,ENST00000477152,;BRCA1,downstream_gene_variant,,ENST00000494123,;BRCA1,downstream_gene_variant,,ENST00000473961,;BRCA1,downstream_gene_variant,,ENST00000497488,;BRCA1,downstream_gene_variant,,ENST00000476777,;BRCA1,3_prime_UTR_variant,,ENST00000461221,;BRCA1,non_coding_transcript_exon_variant,,ENST00000467274,;BRCA1,downstream_gene_variant,,ENST00000492859,;BRCA1,downstream_gene_variant,,ENST00000412061,; A ENSG00000012048 ENST00000357654 Transcript stop_gained 4086/7094 3967/5592 1323 Q/* Caa/Taa rs80357262 1 BRCA1 HGNC 1100 protein_coding CCDS11453.1 ENSP00000350283 BRCA1_HUMAN Q9UE29_HUMAN,Q9NQR3_HUMAN,Q92897_HUMAN,Q7KYU6_HUMAN,Q4EW25_HUMAN,Q3YB53_HUMAN,Q3YB50_HUMAN,Q3YB49_HUMAN,Q3LRH8_HUMAN,Q3B891_HUMAN,K7EPC7_HUMAN,K4K7V3_HUMAN,K4JXS7_HUMAN,K4JUB1_HUMAN,G4V503_HUMAN,G4V502_HUMAN,G4V500_HUMAN,G4V4Z8_HUMAN,G4V4Z7_HUMAN,G1UI37_HUMAN,E9PFZ0_HUMAN,E7EWN5_HUMAN,E7EP70_HUMAN,C9IZW4_HUMAN,C4PFY7_HUMAN UPI0000126AC8 NM_007294.3 23-Oct PIRSF_domain:PIRSF001734,hmmpanther:PTHR13763,hmmpanther:PTHR13763:SF0 not_provided,pathogenic HIGH SNV 1 17 41243581 41243581 G A SNP BRCA1 NM_007294.3 human genbank 58_37c -1 reviewed nonsense c.3967 p.Q1323* 0.949 HMMPfam_BRCT|7CHMMSmart_SM00292|7Csuperfamily_BRCT domain|7CHMMSmart_SM00184|7CPatternScan_ZF_RING_1|7CHMMPfam_zf-C3HC4|7Csuperfamily_RING/U-box - 17 41243581 41243581 G A SNP BRCA1 NM_007294.3 human genbank 58_37c -1 reviewed nonsense c.3967 p.Q1323* 0.949 HMMPfam_BRCT|7CHMMSmart_SM00292|7Csuperfamily_BRCT domain|7CHMMSmart_SM00184|7CPatternScan_ZF_RING_1|7CHMMPfam_zf-C3HC4|7Csuperfamily_RING/U-box - Putative_Driver Test driver Class 1 Class annotation BRCA1 genome.wustl.edu GRCh37 17 41201181 41201181 0 Missense_Mutation SNP C C A rs80357069 byCluster TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 C C Unknown Somatic Phase_IV Capture 1 dbGAP Illumina GAIIx medium 2.25 getma.org/?cm=msa&ty=f&p=BRCA1_HUMAN&rb=1756&re=1842&var=G1788V getma.org/pdb.php?prot=BRCA1_HUMAN&from=1756&to=1842&var=G1788V getma.org/?cm=var&var=hg19,17,41201181,C,A&fts=all ENST00000357654.3:c.5363G>T p.Gly1788Val p.G1788V ENST00000357654 21/23 0 0 BRCA1,missense_variant,p.Gly1492Val,ENST00000309486,NM_007297.3;BRCA1,missense_variant,p.Gly1788Val,ENST00000357654,NM_007294.3;BRCA1,missense_variant,p.Gly1549Val,ENST00000346315,;BRCA1,missense_variant,p.Gly1523Val,ENST00000354071,;BRCA1,missense_variant,p.Gly1809Val,ENST00000471181,NM_007300.3;BRCA1,missense_variant,p.Gly1741Val,ENST00000493795,;BRCA1,missense_variant,p.Gly646Val,ENST00000352993,;BRCA1,missense_variant,p.Gly605Val,ENST00000351666,;BRCA1,missense_variant,p.Gly684Val,ENST00000491747,NM_007298.3;BRCA1,missense_variant,p.Gly279Val,ENST00000591534,;BRCA1,missense_variant,p.Gly98Val,ENST00000586385,;BRCA1,missense_variant,p.Gly21Val,ENST00000591849,;BRCA1,intron_variant,,ENST00000468300,NM_007299.3;BRCA1,3_prime_UTR_variant,,ENST00000461221,; A ENSG00000012048 ENST00000357654 Transcript missense_variant 5482/7094 5363/5592 1788 G/V gGt/gTt rs80357069,COSM436662 1 BRCA1 HGNC 1100 protein_coding CCDS11453.1 ENSP00000350283 BRCA1_HUMAN Q9UE29_HUMAN,Q9NQR3_HUMAN,Q92897_HUMAN,Q7KYU6_HUMAN,Q4EW25_HUMAN,Q3YB53_HUMAN,Q3YB50_HUMAN,Q3YB49_HUMAN,Q3LRH8_HUMAN,Q3B891_HUMAN,K7EPC7_HUMAN,K4K7V3_HUMAN,K4JXS7_HUMAN,K4JUB1_HUMAN,G4V503_HUMAN,G4V502_HUMAN,G4V500_HUMAN,G4V4Z8_HUMAN,G4V4Z7_HUMAN,G1UI37_HUMAN,E9PFZ0_HUMAN,E7EWN5_HUMAN,E7EP70_HUMAN,C9IZW4_HUMAN,C4PFY7_HUMAN UPI0000126AC8 NM_007294.3 deleterious(0) benign(0.031) 21/23 Gene3D:3.40.50.10190,Pfam_domain:PF00533,PIRSF_domain:PIRSF001734,Prints_domain:PR00493,PROSITE_profiles:PS50172,hmmpanther:PTHR13763,hmmpanther:PTHR13763:SF0,SMART_domains:SM00292,Superfamily_domains:SSF52113 not_provided,pathogenic 0,1 MODERATE SNV 1,1 17 41201181 41201181 C A SNP BRCA1 NM_007294 human genbank 57_37b -1 reviewed missense c.5363 p.G1788V 1 HMMPfam_BRCT,HMMSmart_SM00292,superfamily_BRCT domain superfamily_RING/U-box,HMMSmart_SM00184,HMMPfam_zf-C3HC4,PatternScan_ZF_RING_1,HMMPfam_BRCT,HMMSmart_SM00292,superfamily_BRCT domain - 17 41201181 41201181 C A SNP BRCA1 NM_007294 human genbank 57_37b -1 reviewed missense c.5363 p.G1788V 1 HMMPfam_BRCT,HMMSmart_SM00292,superfamily_BRCT domain superfamily_RING/U-box,HMMSmart_SM00184,HMMPfam_zf-C3HC4,PatternScan_ZF_RING_1,HMMPfam_BRCT,HMMSmart_SM00292,superfamily_BRCT domain - -ATM genome.wustl.edu GRCh37 11 108173702 108173702 0 Frame_Shift_Del DEL G G - TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 - G Unknown Germline Phase_IV Capture 1 dbGAP IlluminaGAIIx ENST00000278616.4:c.5443delG p.Asp1815ThrfsTer13 p.D1815Tfs*13 ENST00000278616 36/63 0 0 ATM,frameshift_variant,p.Asp1815ThrfsTer13,ENST00000278616,NM_000051.3;ATM,frameshift_variant,p.Asp1815ThrfsTer13,ENST00000452508,;ATM,non_coding_transcript_exon_variant,,ENST00000524792,;ATM,non_coding_transcript_exon_variant,,ENST00000533690,;ATM,non_coding_transcript_exon_variant,,ENST00000534625,;ATM,upstream_gene_variant,,ENST00000529588,; - ENSG00000149311 ENST00000278616 Transcript frameshift_variant 5827/13147 5442/9171 1814 L/X ttG/tt rs772138812 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 ATM_HUMAN M0QXY8_HUMAN,E9PRG7_HUMAN,E9PIN0_HUMAN UPI0000DBEF44 NM_000051.3 36/63 hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF66 HIGH 1 deletion 1 11 108173702 108173702 G - DEL ATM NM_000051.3 human genbank 58_37c 1 reviewed frame_shift_del c.5442 p.D1815fs 1 superfamily_ARM repeat superfamily_ARM repeat|7CHMMPfam_FAT|7Csuperfamily_Protein kinase-like (PK-like)|7CHMMPfam_PI3_PI4_kinase|7CHMMSmart_SM00146|7CPatternScan_PI3_4_KINASE_1|7CPatternScan_PI3_4_KINASE_2|7CHMMPfam_FATC - 11 108173702 108173702 G - DEL ATM NM_000051.3 human genbank 58_37c 1 reviewed frame_shift_del c.5442 p.D1815fs 1 superfamily_ARM repeat superfamily_ARM repeat|7CHMMPfam_FAT|7Csuperfamily_Protein kinase-like (PK-like)|7CHMMPfam_PI3_PI4_kinase|7CHMMSmart_SM00146|7CPatternScan_PI3_4_KINASE_1|7CPatternScan_PI3_4_KINASE_2|7CHMMPfam_FATC - +ATM genome.wustl.edu GRCh37 11 108173702 108173702 0 Frame_Shift_Del DEL G G - TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 - G Unknown Somatic Phase_IV Capture 1 dbGAP IlluminaGAIIx ENST00000278616.4:c.5443delG p.Asp1815ThrfsTer13 p.D1815Tfs*13 ENST00000278616 36/63 0 0 ATM,frameshift_variant,p.Asp1815ThrfsTer13,ENST00000278616,NM_000051.3;ATM,frameshift_variant,p.Asp1815ThrfsTer13,ENST00000452508,;ATM,non_coding_transcript_exon_variant,,ENST00000524792,;ATM,non_coding_transcript_exon_variant,,ENST00000533690,;ATM,non_coding_transcript_exon_variant,,ENST00000534625,;ATM,upstream_gene_variant,,ENST00000529588,; - ENSG00000149311 ENST00000278616 Transcript frameshift_variant 5827/13147 5442/9171 1814 L/X ttG/tt rs772138812 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 ATM_HUMAN M0QXY8_HUMAN,E9PRG7_HUMAN,E9PIN0_HUMAN UPI0000DBEF44 NM_000051.3 36/63 hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF66 HIGH 1 deletion 1 11 108173702 108173702 G - DEL ATM NM_000051.3 human genbank 58_37c 1 reviewed frame_shift_del c.5442 p.D1815fs 1 superfamily_ARM repeat superfamily_ARM repeat|7CHMMPfam_FAT|7Csuperfamily_Protein kinase-like (PK-like)|7CHMMPfam_PI3_PI4_kinase|7CHMMSmart_SM00146|7CPatternScan_PI3_4_KINASE_1|7CPatternScan_PI3_4_KINASE_2|7CHMMPfam_FATC - 11 108173702 108173702 G - DEL ATM NM_000051.3 human genbank 58_37c 1 reviewed frame_shift_del c.5442 p.D1815fs 1 superfamily_ARM repeat superfamily_ARM repeat|7CHMMPfam_FAT|7Csuperfamily_Protein kinase-like (PK-like)|7CHMMPfam_PI3_PI4_kinase|7CHMMSmart_SM00146|7CPatternScan_PI3_4_KINASE_1|7CPatternScan_PI3_4_KINASE_2|7CHMMPfam_FATC - ATM genome.wustl.edu GRCh37 11 108106472 108106472 0 Frame_Shift_Del DEL T T - novel unknown TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 T T Unknown Somatic Phase_IV Capture 1 dbGAP Illumina GAIIx ENST00000278616.4:c.409delT p.Tyr137ThrfsTer16 p.Y137Tfs*16 ENST00000278616 May-63 0 0 ATM,frameshift_variant,p.Tyr137ThrfsTer16,ENST00000278616,NM_000051.3;ATM,frameshift_variant,p.Tyr137ThrfsTer16,ENST00000452508,;ATM,frameshift_variant,p.Tyr137ThrfsTer16,ENST00000527805,;ATM,intron_variant,,ENST00000527891,;ATM,downstream_gene_variant,,ENST00000601453,;ATM,non_coding_transcript_exon_variant,,ENST00000530958,; - ENSG00000149311 ENST00000278616 Transcript frameshift_variant 792/13147 407/9171 136 I/X aTt/at COSM428356,COSM1474979 1 ATM HGNC 795 protein_coding YES CCDS31669.1 ENSP00000278616 ATM_HUMAN M0QXY8_HUMAN,E9PRG7_HUMAN,E9PIN0_HUMAN UPI0000DBEF44 NM_000051.3 May-63 Pfam_domain:PF11640,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF66 1,1 HIGH 1 deletion 2 1,1 11 108106472 108106472 T - DEL ATM NM_000051 human genbank 57_37b 1 reviewed frame_shift_del c.407 p.Y137fs 0.013 superfamily_ARM repeat,HMMPfam_FAT,superfamily_Protein kinase-like (PK-like),HMMPfam_PI3_PI4_kinase,HMMSmart_SM00146,PatternScan_PI3_4_KINASE_1,PatternScan_PI3_4_KINASE_2,HMMPfam_FATC (deletion:cds_exon[108106397,108106561]) 11 108106472 108106472 T - DEL ATM NM_000051 human genbank 57_37b 1 reviewed frame_shift_del c.407 p.Y137fs 0.013 superfamily_ARM repeat,HMMPfam_FAT,superfamily_Protein kinase-like (PK-like),HMMPfam_PI3_PI4_kinase,HMMSmart_SM00146,PatternScan_PI3_4_KINASE_1,PatternScan_PI3_4_KINASE_2,HMMPfam_FATC (deletion:cds_exon[108106397,108106561]) -BRCA2 genome.wustl.edu GRCh37 13 108106473 108106473 0 Nonsense_Mutation SNP T T C TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 Germline p.D191G BRCA2_HUMAN +BRCA2 genome.wustl.edu GRCh37 13 108106473 108106473 0 Nonsense_Mutation SNP T T C TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 Somatic p.D191G BRCA2_HUMAN BRCA2 genome.wustl.edu GRCh37 13 108106474 108106474 0 Nonsense_Mutation SNP T T C TCGA-A2-A04P-01 TCGA-A2-A04P-10 Somatic p.D191G BRCA2_HUMAN -BRCA2 genome.wustl.edu GRCh37 13 108106475 108106475 0 In_Frame_Del DEL T T - TCGA-A1-A0SK-01 TCGA-A1-A0SK-10 Germline p.R2659T BRCA2_HUMAN +BRCA2 genome.wustl.edu GRCh37 13 108106475 108106475 0 In_Frame_Del DEL T T - TCGA-A1-A0SK-01 TCGA-A1-A0SK-10 Somatic p.R2659T BRCA2_HUMAN BRCA2 genome.wustl.edu GRCh37 13 108106476 108106476 0 In_Frame_Del DEL T T - TCGA-A2-A0CM-01 TCGA-A2-A0CM-10 Somatic p.R2659T BRCA2_HUMAN -BRCA2 genome.wustl.edu GRCh37 13 108106477 108106477 0 Missense_Mutation SNP T T C TCGA-AR-A1AR-01 TCGA-AR-A1AR-10 Germline p.R2336C BRCA2_HUMAN +BRCA2 genome.wustl.edu GRCh37 13 108106477 108106477 0 Missense_Mutation SNP T T C TCGA-AR-A1AR-01 TCGA-AR-A1AR-10 Somatic p.R2336C BRCA2_HUMAN BRCA2 genome.wustl.edu GRCh37 13 108106478 108106478 0 Missense_Mutation SNP T T C TCGA-B6-A0WX-01 TCGA-B6-A0WX-10 Somatic p.R2336C BRCA2_HUMAN -BRCA2 genome.wustl.edu GRCh37 13 108106479 108106479 0 Nonsense_Mutation SNP T T C TCGA-BH-A1F0-01 TCGA-BH-A1F0-10 Germline p.R2000T BRCA2_HUMAN +BRCA2 genome.wustl.edu GRCh37 13 108106479 108106479 0 Nonsense_Mutation SNP T T C TCGA-BH-A1F0-01 TCGA-BH-A1F0-10 Somatic p.R2000T BRCA2_HUMAN BRCA2 genome.wustl.edu GRCh37 13 108106480 108106480 0 Nonsense_Mutation SNP T T C TCGA-B6-A0I6-01 TCGA-B6-A0I6-10 Somatic p.R2000T BRCA2_HUMAN -BRCA2 genome.wustl.edu GRCh37 13 108106481 108106481 0 In_Frame_Del DEL T T - TCGA-BH-A18V-01 TCGA-BH-A18V-10 Germline p.V1270del BRCA2_HUMAN +BRCA2 genome.wustl.edu GRCh37 13 108106481 108106481 0 In_Frame_Del DEL T T - TCGA-BH-A18V-01 TCGA-BH-A18V-10 Somatic p.V1270del BRCA2_HUMAN BRCA2 genome.wustl.edu GRCh37 13 108106482 108106482 0 In_Frame_Del DEL T T - TCGA-BH-A18K-01 TCGA-BH-A18K-10 Somatic p.V1270del BRCA2_HUMAN -BRCA2 genome.wustl.edu GRCh37 13 108106483 108106483 0 Missense_Mutation SNP T T C TCGA-BH-A0HL-01 TCGA-BH-A0HL-10 Germline p.D3073G BRCA2_HUMAN +BRCA2 genome.wustl.edu GRCh37 13 108106483 108106483 0 Missense_Mutation SNP T T C TCGA-BH-A0HL-01 TCGA-BH-A0HL-10 Somatic p.D3073G BRCA2_HUMAN BRCA2 genome.wustl.edu GRCh37 13 108106484 108106484 0 Missense_Mutation SNP T T C TCGA-BH-A0E0-01 TCGA-BH-A0E0-10 Somatic p.D3073G BRCA2_HUMAN ACP3 genome.wustl.edu GRCh37 3 132047117 132047117 0 Missense_Mutation SNP C C T TEST_SAMPLE_1 Somatic NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000336375.5:c.127C>T p.Arg43Trp p.R43W ENST00000336375 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PPAP_HUMAN NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ACP3 genome.wustl.edu GRCh37 3 132047117 132047117 0 Missense_Mutation SNP C C T TEST_SAMPLE_2 Somatic NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000336375.5:c.127C>T p.Arg43Trp p.R43W ENST00000336375 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PPAP_HUMAN NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ACP3 genome.wustl.edu GRCh37 3 132047117 132047117 0 Missense_Mutation SNP C C T TEST_SAMPLE_3 Somatic NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000336375.5:c.127C>T p.Arg43Trp p.R43W ENST00000336375 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PPAP_HUMAN NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ACP3 genome.wustl.edu GRCh37 3 132047117 132047117 0 Missense_Mutation SNP C C T TEST_SAMPLE_4 Somatic NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000336375.5:c.127C>T p.Arg43Trp p.R43W ENST00000336375 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PPAP_HUMAN NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA -ACP3 genome.wustl.edu GRCh37 3 132047117 132047117 0 Missense_Mutation SNP C C T TEST_SAMPLE_15 Somatic NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000336375.5:c.127C>T p.Arg43Trp p.R43W ENST00000336375 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PPAP_HUMAN NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA +ACP3 genome.wustl.edu GRCh37 3 132047117 132047117 0 Missense_Mutation SNP C C T TEST_SAMPLE_15 Somatic NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENST00000336375.5:c.127C>T p.Arg43Trp p.R43W ENST00000336375 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PPAP_HUMAN NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA \ No newline at end of file diff --git a/tests/unit_tests_validate_data.py b/tests/unit_tests_validate_data.py index 3089d33b..11c77303 100755 --- a/tests/unit_tests_validate_data.py +++ b/tests/unit_tests_validate_data.py @@ -1897,14 +1897,23 @@ def test_validation_ms(self): record_list = self.validate('mutations/data_mutations_ms.maf', validateData.MutationsExtendedValidator, extra_meta_fields={'swissprot_identifier': 'name'}) - # we expect 1 warning - self.assertEqual(1, len(record_list)) + # we expect 2 warnings + self.assertEqual(2, len(record_list)) # Check warning message - self.assertEqual(logging.WARNING, record_list[0].levelno) - self.assertEqual(2, record_list[0].line_number) - self.assertEqual('test', record_list[0].cause) - self.assertEqual("Mutation_Status value is not in MAF format", record_list[0].getMessage()) + record_iterator = iter(record_list) + record = next(record_iterator) + # Expected warning message due to value "test" in Mutation_Status + self.assertEqual(logging.WARNING, record.levelno) + self.assertEqual(2, record.line_number) + self.assertEqual('test', record.cause) + self.assertEqual("Mutation_Status value is not in MAF format", record.getMessage()) + # Expected warning message due to value "Germine" in Mutation_Status + record = next(record_iterator) + self.assertEqual(logging.WARNING, record.levelno) + self.assertEqual(4, record.line_number) + self.assertEqual('Germline', record.cause) + self.assertEqual("GERMLINE variant identified from the Mutation_Status value. If this variant is not meant for public release, please remove it.", record.getMessage()) def test_mutation_not_loaded_ms(self): @@ -1916,7 +1925,8 @@ def test_mutation_not_loaded_ms(self): extra_meta_fields={'swissprot_identifier': 'name'}) # We expect 5 info messages, 3 from not loaded mutations and 2 general lines - self.assertEqual(5, len(record_list)) + # We expect 1 warning message for the germline variant + self.assertEqual(6, len(record_list)) record_iterator = iter(record_list) # Expected info message due to value "None" in Mutation_Status record = next(record_iterator) @@ -1930,6 +1940,12 @@ def test_mutation_not_loaded_ms(self): self.assertEqual(5, record.line_number) self.assertEqual('loh', record.cause) self.assertEqual("Mutation will not be loaded due to value in Mutation_Status", record.getMessage()) + # Expected warning message due to value "Germline" in Mutation_Status + record = next(record_iterator) + self.assertEqual(logging.WARNING, record.levelno) + self.assertEqual(7, record.line_number) + self.assertEqual('Germline', record.cause) + self.assertEqual("GERMLINE variant identified from the Mutation_Status value. If this variant is not meant for public release, please remove it.", record.getMessage()) # Expected info message due to value "Wildtype" in Mutation_Status record = next(record_iterator) self.assertEqual(logging.INFO, record.levelno)