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Ensembl / ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
https://www.ensembl.org/vep
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upstream_gene_variant with distance 0 #1147

Open 0xaf1f opened 2 years ago

0xaf1f commented 2 years ago

Describe the issue

We noticed a variant, a single base insertion after the first position of a gene, getting annotated as an upstream_gene_variant with respect to that gene. The distance is then 0 since it's not actually upstream, but why isn't it instead called a frameshift mutation?

This is the problematic annotation:

A|upstream_gene_variant|MODIFIER|dxs2|Rv3379c|Transcript|CCP46200|protein_coding|||||||||||0|-1||1|insertion|ENA_GENE|

Additional information

System

Full VEP command line

vep --force_overwrite --dir /path/to/.vep --synonyms /path/to/.vep/synonyms.txt --offline --cache --cache_version 30 --species mycobacterium_tuberculosis_h37rv --symbol --variant_class --flag_pick --vcf -i test-case.vcf -o test-case.annotated.vcf

Full error message

N/A

Data files (if applicable)

vep-distance-issue.tar.gz

diegomscoelho commented 2 years ago

Hi @0xaf1f,

We are currently investigating your issue. I will post an answer here shortly.

Thanks for your question.

Regards, @diegomscoelho