[ensembl-dev] [VEP] Clean Insertion before start codon

João Eiras joao.eiras at gmail.com
Tue Jan 31 18:27:36 GMT 2017


Hi.

I have the following variant from cosmic [1]

X       109475934       COSM4612273     C       CATA

This is a clean insertion over the start codon of transcript ENSMUST00000086738

ATG -> ATA ATG

The annotation's JSON looks like:
"amino_acids": "M/IM",
"cdna_end": 295,
"cdna_start": 294,
"cds_end": 3,
"cds_start": 2,
"codons": "atg/atTATg",
"consequence_terms": ["start_lost"],
"impact": "HIGH",
"protein_end": 1,
"protein_start": 1,
"strand": -1,
"transcript_id": "ENST00000218006",
"variant_allele": "ATA",

You can see the consequence is a simple start_loss. In this case, the
start codon is preserved, and from the point of view of translation,
having 3 extra nucleotides before the start codon is most likely not
to have any impact.

As such, I think the consequence_terms should be something like
start_retained_variant+inframe_insertion+5_prime_UTR_variant. Since
the start is preserved, the new nucleotides will just stay in the UTR.

Thoughts ?

Thank you.

[1] https://cancer.sanger.ac.uk/cosmic/download




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