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!
You might find a tool like "TransVar" to be useful: https://bioinformatics.mdanderson.org/transvar/
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:
Thanks a lot, really helpful!