[ensembl-dev] Seemingly incorrect HGVS for RefSeq on GRCh37

Wallace Ko myko at l3-bioinfo.com
Mon Feb 18 14:57:29 GMT 2019


When the variant '11 70742675 G/A' is annotated with VEP, there are 2
results with high and moderate impact:

   1. NM_012309.4:c.958C>T (cDNA position: 1070)
   2. NM_012309.3:c.959C>T (cDNA position: 1037)

For the first result, the actual nucleotide at NM_012309.4:n.1070 is T. May
I assume that the FAILED value in BAM EDIT field indicates that the HGVS is

For the second result, the actual nucleotide at NM_012309.3:n.1037 is A.
And the result of blat on NC_000011.9 show that NM_012309.3:n.1037 aligns
to nowhere. I wonder how VEP would produce result. And do you have any
suggested practice to filter them?

Wallace Ko
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20190218/527f97a6/attachment.html>

More information about the Dev mailing list