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

Question

[a615ebfb]

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

Answer 1

[Jeremy Leipzig]

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

[a615ebfb]

Thanks, Jeremy! Not sure if I retrieved the right one but it does not show up as pathogenic on the website: https://www.ncbi.nlm.nih.gov/clinvar/variation/242687/?oq=242687&m=NM_000570.4(FCGR3B):c.316A=%20(p.Ile106=)

Additionally, perhaps I should be more specific- does anyone know of any polymorphic pathogenic ClinVar variants where the hg38 reference allele is pathogenic?

[GenoMax]

It is likely this one --> https://www.ncbi.nlm.nih.gov/clinvar/variation/36924/

From original search here --> https://www.ncbi.nlm.nih.gov/clinvar/?term=NC_000001.11:g.161629781

[a615ebfb]

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