Question: variant REF-ALT conversion to HGVS.c
gravatar for cocchi.e89
9 months ago by
cocchi.e8930 wrote:

Dear all,

I am quite new so sorry if this is a silly question. I am working on a VCF files and comparing my variant with GnomAD DB. I noticed that the VEP column of Gnomad HGVS.c bases are different from the REF-ALT bases.

As example, GnomAD DB row:

21 10944679 rs770820681 C A 3696.48 RF AC=1 ... vep=A|missense_variant|MODERATE|TPTE|ENSG00000166157|Transcript|ENST00000298232|protein_coding|10/23||ENST00000298232.7:c.501G>T|ENSP00000298232.7:p.Arg167Ser...

The variant is a C>A and the VEP column is referring to A allele (first VEP field), but it points to a transcript with a change G>T.

How is that possible? What the "conversion" between them?

Thanks a lot in advance for any help!

variants nomeclature hgvs gene • 394 views
ADD COMMENTlink modified 9 months ago by Pierre Lindenbaum125k • written 9 months ago by cocchi.e8930

You might find a tool like "TransVar" to be useful:

Say you start with the HGVS.c notation (ENST00000298232.7:c.501G>T), select "Reverse annotation: cDNA", some reference genome (e.g. GRCh37) and in this case use Ensembl as the annotation database. Enter "ENST00000298232.7:c.501G>T" as the query and it'll give you the different representations between genomic, cDNA, protein variant formats:

input   transcript  gene    strand  coordinates(gDNA/cDNA/protein)  region  info
ENST00000298232.7:c.501G>T  ENST00000298232 (protein_coding)    TPTE    -   chr21:g.10944679C>A/c.501G>T/p.R167S    inside_[cds_in_exon_10] CSQN=Missense;dbsnp=rs770820681(chr21:10944679C>A);reference_codon=AGG;alternative_codon=AGT;aliases=ENSP00000298232;source=Ensembl
ADD REPLYlink written 9 months ago by manuel.belmadani1.2k

Thanks a lot, really helpful!

ADD REPLYlink written 9 months ago by cocchi.e8930
gravatar for Pierre Lindenbaum
9 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum125k wrote:

How is that possible? What the "conversion" between them?

ENSG00000166157 is mapped on the reverse strand in grch37;r=21:10906201-11029719

ADD COMMENTlink written 9 months ago by Pierre Lindenbaum125k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1066 users visited in the last hour