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Example of ClinVar pathogenic variant where the reference allele is pathogenic?

Hello, Can someone point me to a ClinVar pathogenic variant where the hg38 reference allele is pathogenic?

snp variant pathogenic clinvar
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updated by tamerg tamerg • written by a615ebfb • a615ebfb

1 answer

For REF/REF entries the ALT is '.'

wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz

gunzip -c "clinvar.vcf.gz" | grep -v "^#" | awk -F'\t' '$5=="." {print}' | grep Pathogenic | head -n 1
1   161629781   242687  T   .   .   .   AF_EXAC=0.66256;ALLELEID=45585;CLNHGVS=NC_000001.11:g.161629781%3D;CLNREVSTAT=no_classification_for_the_single_variant;CLNSIG=no_classification_for_the_single_variant;CLNVC=single_nucleotide_variant;CLNVCSO=SO:0001483;CLNVI=OMIM:610665.0001;GENEINFO=FCGR3B:2215;MC=SO:0002073|no_sequence_alteration;ONC=no_classification_for_the_single_variant;ONCREVSTAT=no_classification_for_the_single_variant;RS=2290834;SCI=no_classification_for_the_single_variant;SCIREVSTAT=no_classification_for_the_single_variant;CLNDISDBINCL=MedGen:C4017227;CLNDNINCL=Neutrophil-specific_antigens_NA1/NA2;CLNSIGINCL=36924:Pathogenic
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written by Jeremy Leipzig Jeremy Leipzig

Thanks for the response. These examples are part of haplotypes so not exactly what I was looking for.

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written by a615ebfb • a615ebfb

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