The team page has been updated to include headshots and bios for gnomAD staff members.
Changelog
The changelog contains a record of all changes made to gnomAD, small or large.
Monoallelic flag added to variant table
The variant table displayed on Gene, Region, and Transcript pages now includes a possible ‘Monoallelic’ flag. This flag labels sites where all samples have homozygous alternate genotypes.
New team page
A new team page centralizes information about the people who work on the gnomAD project. Pertinent information that was previously located on the About page has been moved to Teams, and additional details about the team have been added.
Update policies page
The policies page, previously titled ‘terms’, has been updated to cover additional policies. New policies include, but are not limited to, data privacy, ethics, and open science.
Zoom in on gene and transcript pages
The gene and transcript pages show variants located in or within 75 bases of a coding exon. For genes and transcripts with large coding regions, this can result in data in the tracks being difficult to see when it is condensed into a small area on the screen. Now, you can zoom in on genes and transcripts to focus on data in a specific region.
gnomAD v3.1.2
The browser has been updated to show data from gnomAD v3.1.2. For more information about changes in this version, see the gnomAD v3.1.2 blog post.
Link to ClinGen Allele Registry added to variant pages
For variants where a ClinGen Canonical Allele ID is available, a link to the ClinGen Allele Registry has been added to the “External Resources” section on the variant page.
Coverage added to variant pages
The mean depth of coverage at a variant’s locus can now be found on the variant page after the variant’s allele frequency information.
MANE transcripts updated to release 0.95
For genes with a MANE Select transcript, the MANE Select transcript is displayed on the gene page. The browser now displays data from MANE release 0.95.
Navigate directly to structural variants
Previously, viewing structural variants in the browser required looking up a gene or region in gnomAD v2 and then switching to the structural variant dataset.
Now, structural variants can be directly navigated to by selecting “gnomAD SVs v2.1” in the search box on the home page.
Population frequencies table moved to the top of the variant page
Responses to our user survey confirmed that population frequencies are one of the most popular and widely used features of gnomAD. Reflecting that, the population frequencies table has been moved to the top of the variant page to make it more easily accessible.
ClinVar variant details available in ClinVar variants track
Detailed information about ClinVar variants, such as submissions, is now available in the ClinVar variants track on gene, region, and transcript pages.
Changes to transcript tissue expression visualization
To help identify biologically relevant transcripts, the gene page includes information from the GTEx project on transcripts’ expression in different tissues.
Transcript expression added to pext track
Transcript tissue expression information from the GTEx project has been added to the individual tissue pext tracks.
Variant co-occurrence (phasing) information added
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.
See more information in the full blog post.
gnomAD-hosted public files moved to requester-pays bucket
We recently removed all gnomAD VCFs from our public buckets, as these files are now hosted via public dataset programs on three major cloud…
Rename filter in mitochondria dataset and minor format changes
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We corrected:
- dbSNP rsIDs. The dbSNP resource we used to annotate rsIDs was not split for multi-allelic variants, so if a variant was…
gnomAD VCFs removed from public bucket
Last year, as part of an effort to reduce costs, we shifted our public Hail-formatted tables into requester-pays buckets. In keeping with our commitment to make gnomAD data as free and accessible to the world as possible, we continued to make VCFs free to download, paying for these downloads ourselves.
Over the last year, we’ve worked with major cloud providers to make these VCFs available for free via their public dataset programs. We’ve decided, as a result, to remove gnomAD VCF files from our own bucket, and encourage users to make use of the (identical) VCF files hosted by our cloud partners.
Liftover
On variant pages you can now quickly switch between genome builds and gnomAD versions using our new liftover feature. This is available on v2 and v3 variants.
gnomAD v3.1.1
gnomAD v3.1.1 contains some minor corrections and changes to the v3.1 data release. The major annotations, including allele count, allele number, and allele frequency, as well as variant filtering status, remain unchanged for the entire callset and for all subsets of the callset (except the change noted below about switching to Null instead of 0).
New help page
A new help page brings together content that was previously divided between different areas of the browser. Now all content, including frequently asked questions and help popups, can be searched in one place.
Additional filters for ClinVar track
The ClinVar track can now be filtered by VEP consequence category (pLoF, missense / inframe indel, synonymous, other) as well as pathogenicity.
Change to population labels
In the population frequencies table for gnomAD v2.1.1 and gnomAD structural variants, we have changed the labels we use to classify individuals by chromosomal sex from “male” and “female” to “XY” and “XX,” respectively. More detail on the reason for this change can be found in the gnomAD v3.1 blog post.
MANE Select / Ensembl canonical transcripts noted on transcript pages
Transcript pages now note if the transcript is the MANE Select or Ensembl canonical transcript for its gene.
Population frequencies for mitochondrial variants
Population frequencies are now available for mitochondrial variants.
Configure variant table columns
The variant table now supports selecting which columns to show and changing the order of columns.
Filter ClinVar track to variants in gnomAD
The ClinVar track can now be filtered to only show ClinVar variants that also appear in gnomAD.