EXON19 FS EGFR variant
Dear professor,
Thanks a lot.
I met a variant called by vardict in EGFR EXON19.
chr7 55242462 . CAAGGAATT C . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=584,592|68,88;DP=1375;ECNT=10;GERMQ=93;MBQ=20,20;MFRL=132,135;MMQ=60,60;MPOS=21;POPAF=7.30;ROQ=93;TLOD=466.36;ANNOVAR_DATE=2020-06-08;Func.refGeneWithVer=exonic;Gene.refGeneWithVer=EGFR;GeneDetail.refGeneWithVer=.;ExonicFunc.refGeneWithVer=frameshift_deletion;AAChange.refGeneWithVer=EGFR:NM_005228.4:exon19:c.2233_2240del:p.E746Rfs*14;1000g2015aug_all=.;AF=.;AF_popmax=.;AF_male=.;AF_female=.;AF_raw=.;AF_afr=.;AF_sas=.;AF_amr=.;AF_eas=.;AF_nfe=.;AF_fin=.;AF_asj=.;AF_oth=.;non_topmed_AF_popmax=.;non_neuro_AF_popmax=.;non_cancer_AF_popmax=.;controls_AF_popmax=.;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;CLNHGVS=.;avsnp150=.;cosmic94=.;Alt=.;#Chr=.;Start=.;DamagePredCount=.;SIFT_pred=.;SIFT4G_pred=.;LRT_pred=.;MutationTaster_pred=.;MutationAssessor_pred=.;FATHMM_pred=.;PROVEAN_pred=.;MetaSVM_pred=.;MetaLR_pred=.;M-CAP_pred=.;MutPred_score=.;MVP_score=.;MPC_score=.;PrimateAI_pred=.;DEOGEN2_pred=.;BayesDel_addAF_pred=.;BayesDel_noAF_pred=.;LIST-S2_pred=.;DANN_score=.;fathmm-MKL_coding_pred=.;fathmm-XF_coding_pred=.;Eigen-raw_coding=.;Eigen-phred_coding=.;Eigen-PC-raw_coding=.;Eigen-PC-phred_coding=.;integrated_fitCons_score=.;GM12878_fitCons_score=.;H1-hESC_fitCons_score=.;HUVEC_fitCons_score=.;GERP++_NR=.;GERP++_RS=.;phyloP100way_vertebrate=.;phyloP30way_mammalian=.;phyloP17way_primate=.;phastCons100way_vertebrate=.;phastCons30way_mammalian=.;phastCons17way_primate=.;bStatistic=.;Interpro_domain=.;GTEx_V8_gene=.;GTEx_V8_tissue=.;ALLELE_END GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:1176,156:0.124:1332:298,45:325,38:734,103:584,592,68,88
chr7 55242490 . A AAAGCCAAC . clustered_events;slippage AS_FilterStatus=SITE;AS_SB_TABLE=446,445|43,42;DP=1104;ECNT=10;GERMQ=93;MBQ=20,20;MFRL=144,147;MMQ=60,60;MPOS=35;POPAF=7.30;ROQ=93;RPA=1,2;RU=AAGCCAAC;STR;STRQ=1;TLOD=289.35;ANNOVAR_DATE=2020-06-08;Func.refGeneWithVer=exonic;Gene.refGeneWithVer=EGFR;GeneDetail.refGeneWithVer=.;ExonicFunc.refGeneWithVer=frameshift_insertion;AAChange.refGeneWithVer=EGFR:NM_005228.4:exon19:c.2260_2261insAAGCCAAC:p.E758Pfs*11;1000g2015aug_all=.;AF=.;AF_popmax=.;AF_male=.;AF_female=.;AF_raw=.;AF_afr=.;AF_sas=.;AF_amr=.;AF_eas=.;AF_nfe=.;AF_fin=.;AF_asj=.;AF_oth=.;non_topmed_AF_popmax=.;non_neuro_AF_popmax=.;non_cancer_AF_popmax=.;controls_AF_popmax=.;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;CLNHGVS=.;avsnp150=.;cosmic94=.;Alt=.;#Chr=.;Start=.;DamagePredCount=.;SIFT_pred=.;SIFT4G_pred=.;LRT_pred=.;MutationTaster_pred=.;MutationAssessor_pred=.;FATHMM_pred=.;PROVEAN_pred=.;MetaSVM_pred=.;MetaLR_pred=.;M-CAP_pred=.;MutPred_score=.;MVP_score=.;MPC_score=.;PrimateAI_pred=.;DEOGEN2_pred=.;BayesDel_addAF_pred=.;BayesDel_noAF_pred=.;LIST-S2_pred=.;DANN_score=.;fathmm-MKL_coding_pred=.;fathmm-XF_coding_pred=.;Eigen-raw_coding=.;Eigen-phred_coding=.;Eigen-PC-raw_coding=.;Eigen-PC-phred_coding=.;integrated_fitCons_score=.;GM12878_fitCons_score=.;H1-hESC_fitCons_score=.;HUVEC_fitCons_score=.;GERP++_NR=.;GERP++_RS=.;phyloP100way_vertebrate=.;phyloP30way_mammalian=.;phyloP17way_primate=.;phastCons100way_vertebrate=.;phastCons30way_mammalian=.;phastCons17way_primate=.;bStatistic=.;Interpro_domain=.;GTEx_V8_gene=.;GTEx_V8_tissue=.;ALLELE_END GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:891,85:0.094:976:241,29:260,23:567,58:446,445,43,42
is this a real variant?
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Thank you for your post, linouhao ! I want to let you know we have received your question and will be moving it to the Community Discussions -> General Discussion topic, as the Somatic topic is for reporting bugs and issues with GATK.
You may be able to find more helpful information on the VarDict GitHub.
We'll get back to you if we have any updates or follow up questions. Please see our Support Policy for more details about how we prioritize responding to questions.
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thanks a lot
sorry, I forgot to revise vardict as gatk, because I used both callers, they all found that
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Hi linouhao,
I'm glad to hear that our documentation was able to help!
I will be closing this ticket now. Please do not hesitate to reply with any questions/issues that may arise in the future.Thank you for being a valued member of our GATK community!
Best,
Anthony
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