New Evidence key - stop codon gained

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New Evidence key - stop codon gained #579

Open davmlaw opened 2 years ago

davmlaw commented 2 years ago

NM_000251.3(MSH2):c.2527delT is annotated as consequence=frameshift in VEP but the p.HGVS has NP_000242.1:p.Cys843Valfs*49

Knowing if it's an early stop or not is important for PVS1

Add a new evidence key that is something like "early stop codon" in "Computational and predictive data" section
Populate this with the 49 from the protein change

There is already "Loss of Function Assertion" - I think we should have a new Ekey as this is human input

davmlaw commented 2 years ago

Can't just get this from consequence as:

NM_000251.3(MSH2):c.2527delT is annotated as consequence=frameshift in VEP but the p.HGVS has NP_000242.1:p.Cys843Valfs*49 - so it should be a stop gained

Re-tested this in VEP 106, and still occurs. Raised issue at Ensembl-vep project