Discordance HGVS name of variant between annovar annotation and ClinVar

Question

[hudahui]

Recently I met the problem of discordance HGVS name of variant between annovar annotation and ClinVar.

I extracted the location of transcripts from latest NCBI GRCh37 refseq annotation and annotate the variants with AnnoVar. But the some entries doesnot match the ClinVar. By counting the CDS location base manually, I found that the result of AnnoVar was correct. Then I used VEP as the third party to asses the result. Surprisingly, The results of VEP overlaped with these two, but most of entries were consistent with Annovar. So anybody met the similar questions, need help~

The detailed table is below.

[GenoMax]

May sound trivial but are you looking at correct genome build in ClinVar?

[hudahui]

Thank you for your kind reply. Yes, I used the GRCh37 version of ClinVar entries, the genomic coordinate, assembly and trancripts version are the same, but the HGVS name differs.

Answer 1

[Jeremy Leipzig]

These discrepancies are concerning.

IMHO VEP is the best at HGVS, better than Annovar. Mutalyzer is also better than Annovar. SnpEff is probably somewhere in the middle, better than Annovar but maybe not as good as Mutalyzer. Hard to say.

ClinVar is just a list, not an annotator, so you'd have to see what tool they actually used. Obviously it is neither Annovar nor VEP but perhaps just done by hand, in which case the right-shifting and "rolling" will be messed up, as discussed here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5267466/

Good question!

[hudahui]

Thank you for your kind reply.

[Ram]

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