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tonydisera
SCN8A missing likely pathogenic ClinVar annotaiton
Al - Do you know if there are any issues with the ClinVar annotations? I just pulled up proband .....52 in study A259. I had this listed as a stop gain, clinvar variant in SCN8A, but I'm not seeing any ClinVar variants in that gene now.
Yes, I see the same issue. Hmm.. We did switch over to using the ClinVar vcf rather than EUTILS to annotate the variants. I will look into this.
The ClinVar annotation used to be in the ClinVar vcf (back in Nov 2016), but is no longer listed in the current ClinVar vcf. I was able to looking it up based on the ClinVar accession number:
https://www.ncbi.nlm.nih.gov/clinvar/RCV000189268.1/
There is a (tiny) ! not current glyph in the top right corner. I'm not sure what the process is in place for getting rid of ClinVar submissions, but I suspect that they are flagged and then removed from the VCF.
In ClinVar, the advanced search based on Chromosome and GRCh37 position returns zero results for this variant. In dbSNP, the ClinVar entry is also omitted.
Ok, two comments:
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Looking at sample ...976 for the same study. Gene SCN2A shows no ClinVar variants, but there is a variant at position 2:166165903 that does appear in a ClinVar search of the SCN2A gene.
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Is there a way of showing ClinVar history? When I look at a sample that I know had a ClinVar variant and I no longer see it, it would be useful to see in the summary that a variant had been removed from ClinVar.
