[ensembl-dev] VEP e!90 HGVS del/dup bases removed?

Sarah Hunt seh at ebi.ac.uk
Mon Dec 11 13:44:00 GMT 2017

Hi Luke,

After discussions with collaborators on the myriad of different ways the 
same allele can be represented in HGVS, we removed the 
deleted/duplicated bases to conform with the recommended rather than 
permitted version of the nomenclature. There isn't a way to include them 
at the moment. This could be added, but it would contribute to the 
difficulty in comparing annotations across different sources.

Best wishes,


On 11/12/2017 13:18, Luke Goodsell wrote:
> Hi,
> We’ve noticed since upgrading from e!88 to e!90 that the 
> deleted/duplicated bases are no longer being reported in HGVS strings. 
> Is there a way to include them?
> Out of curiosity, why were they removed? It was my understanding that 
> they are not required by the HGVS spec, but that they can be 
> optionally included. We use them downstream as a way to double-check 
> the variant annotation.
> Kind regards,
> Luke
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