variant REF-ALT conversion to HGVS.c
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4.5 years ago
cocchi.e89 ▴ 240

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!

gene hgvs nomeclature variants • 1.5k views
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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:

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
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Thanks a lot, really helpful!

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4.5 years ago

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

ENSG00000166157 is mapped on the reverse strand in grch37 http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000166157;r=21:10906201-11029719

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