Gene Variant Image retirement for human, e93

As of Ensembl release 93, which is due at the end of the month, the Gene Variant Image view will be retired for human. We have elected to retire this page because we feel that the density of known genetic variation is too great for this view to be informative in its current form.

The Variant Image page for human BRCA2 in Ensembl 92. The sheer number of variants makes it difficult to pull any information out of this view.

The Variant Image view displays the genetic variants across the different transcripts of the gene by highlighting their location against the block and linker models of the transcripts. When this image was first designed, there were few known variants in human, and it was an informative way to look at genetic variation. Indeed for many species, where less is known about the genetic variation, it is still a very useful way to visualise variants in genes.

However, since projects such as the 1000 Genomes and gnomAD have exploded the number of known genetic variants in human, the view has become a glorious mess of colour, which is very hard to get any information from. With Ensembl 93 comes another update from gnomAD, which will double the number of known genetic variants in the database. For this reason, we have decided to retire this view in human only.

The data is not lost, however. You can still find all the variants in a gene via our Variant Table, which allows you to sort and filter the variants by location within the gene, consequence and evidence, and view them on the gene Sequence.The similar Transcript Variation view will remain active.

If this view is vitally important for your work, please get in touch as soon as possible, to let us know how you use it.

Long-term, we are looking into better ways to graphically display variants against gene and transcript structure, and would be keen to have your input on how we do this. Please fill in this form if you’d like to help out.