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Ensembl VEP cannot parse HGVS notation.

Hello.

So I used VEP to analyze ENST to refseq transcripts in terms of position differences between them. However when I run my HGVS notations through VEP I get these errors (for HBA1 gene, if that helps).

WARNING: Unable to parse HGVS notation 'ENST00000320868:c.-52C>T'

WARNING: Unable to parse HGVS notation 'ENST00000320868:c.-42C>T'

All of the other HGVS work in the file. I'm curious as to why this is occuring, furthermore I have noticed in happen in some other files but not all.

Any insight would certainly be appreciated! :)

vep hgvs ref_seq parsing ensembl
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updated by zx8754 zx8754 • written by gmora • gmora

1 answer

Solved it appears as though the ENST transcript have slightly different naming conventions for variants in the UTR regions.

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written by gmora • gmora

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