Question: Discordance HGVS name of variant between annovar annotation and ClinVar
1
gravatar for hudahui
5 weeks ago by
hudahui10
hudahui10 wrote:

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.

table

snp • 114 views
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by hudahui10

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

ADD REPLYlink written 5 weeks ago by genomax85k

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.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by hudahui10
1
gravatar for Jeremy Leipzig
5 weeks ago by
Philadelphia, PA
Jeremy Leipzig19k wrote:

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!

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by Jeremy Leipzig19k

Thank you for your kind reply.

ADD REPLYlink written 5 weeks ago by hudahui10

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they work.

Upvote|Bookmark|Accept

ADD REPLYlink written 5 weeks ago by RamRS27k
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