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Update Ensembl VEP help page #1835

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7038aac
update vep to include note about RNU4ATAC and also rename VEP>Ensembl…
ch-kr Jan 12, 2026
f0dc234
add note about GENCODE basic, also HT only
ch-kr Jan 22, 2026
a1d7a95
update note about RNU4ATAC
ch-kr Jan 30, 2026
6ab3a05
4.1 > 4.1.1
ch-kr Mar 13, 2026
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6 changes: 4 additions & 2 deletions browser/help/topics/vep.md
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Expand Up @@ -5,9 +5,11 @@ title: 'Annotations in gnomAD'

### gnomAD v4.1

#### VEP
#### Ensembl VEP

Variants in the browser (and all current VCFs available for download) were annotated using VEP version 105 using GENCODE v39 on GRCh38, with the [LOFTEE](https://github.com/konradjk/loftee) (Loss-Of-Function Transcript Effect Estimator) plugin.
Variants in the browser (and all current VCFs available for download) were annotated using Ensembl VEP version 105 using GENCODE v39 on GRCh38, with the [LOFTEE](https://github.com/konradjk/loftee) (Loss-Of-Function Transcript Effect Estimator) plugin.

Note that only variants in the gene [RNU4ATAC](https://gnomad.broadinstitute.org/gene/ENSG00000264229?dataset=gnomad_r4) were annotated using Ensembl VEP version 115 (GENCODE v49 on GRCh38) on the browser. Ensembl VEP version 115 annotations for other [GENCODE basic transcripts](https://www.gencodegenes.org/pages/faq.html) are available in our [downloadable Hail Tables](https://gnomad.broadinstitute.org/data#v4). We are not currently planning to update the Ensembl VEP version for other genes in the gnomAD browser.

#### <a name="loftee"></a>LOFTEE

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