Today, we released gnomAD v4.1.1, which includes an update to our gene constraint metrics, LOFTEE flags, and a minor update to other flags and annotations. In this blog post, we discuss the improvements incorporated in this release, our new LOEUF threshold recommendations, and guidance around interpretation of the gene constraint metrics.

We have released a new utility, the gnomAD toolbox, to enable easier analysis of gnomAD data. Community feedback has highlighted challenges…

We have released gnomAD v4.1, an update to our latest major release. This update fixes the allele number issue in gnomAD v4.0 previously…

We updated our gene constraint metrics following the release of gnomAD v4.0. gnomAD v4.0 expanded the scale of our constraint calculations…

In this minor release of gnomAD v3.1, we include the following improvements to the previous release: a fix to the homozygous alternate allele depletion adjustment that was made for v3.1 and several updates to the gnomAD v3.1 Human Genome Diversity Project (HGDP) and 1000 Genomes (1KG) subset release. 

By popular request, we are now releasing the genetic ancestry principal components analysis (PCA) variant loadings and accompanying random forest (RF) model used for genetic ancestry group inference in gnomAD v2 and v3. This post discusses how those files were generated and how they can be used on another dataset. However, the use of these resources will not be appropriate for all datasets, and therefore we are including a discussion of the caveats associated with using these loadings and the RF model.

Today, we are pleased to announce the incorporation of variant co-occurrence (inferred phasing) information in the gnomAD v2 browser. Phase refers to the genetic relationship between a pair of variants; that is, whether the variants are on the same copy of the gene (cis) or on different copies of the gene (trans). We are releasing inferred phasing data for all pairs of variants within a gene where both variants have a global allele frequency in gnomAD exomes <5% and are either coding, flanking intronic (from position -1 to -3 in acceptor sites, and +1 to +8 in donor sites) or in the 5’/3’ UTRs. This encompasses 20,921,100 pairs of variants across 19,685 genes. We envision that this data will be of tremendous help to the medical genetics community in identifying and interpreting co-occurring variants in the context of recessive conditions.

We’re proud to announce the gnomAD v3.1 release of 759,302,267 short nuclear variants (644,267,978 passing variant quality filters) observed in 76,156 genome samples.

In this release, we have included more than 3,000 new samples specifically chosen to increase the ancestral diversity of the resource. As a result, this is the first release for which we have a designated population label for samples of Middle Eastern ancestry, and we are thrilled to be able to include these in the following population breakdown for the v3.1 release: