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Jan 30, 2026
browser/help/topics/vep.md
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| 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. | ||
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| Note that 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. 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. |
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should we say why just RNU4ATAC is different?
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could also clarify if the RNU4ATAC changes apply to brower/downloads
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I was hoping to avoid emphasizing RNU4ATAC too much, since I don't want to set the precedent that we can go back and fix annotations for single genes (it's not sustainable). I've slightly updated the note though, let me know what you think!
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wasn't sure if that was the case, sounds good!
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Add "Ensembl", also add note about RNU4ATAC and VEP 115 in downloads