[ensembl-dev] Seemingly incorrect HGVS for RefSeq on GRCh37
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?
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the Dev