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.
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.
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.
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.
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.
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.
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.
Detailed information about ClinVar variants, such as submissions, is now available in the ClinVar variants track on gene, region, and transcript pages.
To help identify biologically relevant transcripts, the gene page includes information from the GTEx project on transcripts’ expression in different tissues.
Transcript tissue expression information from the GTEx project has been added to the individual tissue pext tracks.
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.
- dbSNP rsIDs. The dbSNP resource we used to annotate rsIDs was not split for multi-allelic variants, so if a variant was…
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.
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 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).
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.
The ClinVar track can now be filtered by VEP consequence category (pLoF, missense / inframe indel, synonymous, other) as well as pathogenicity.
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.
Population frequencies are now available for mitochondrial variants.
The variant table now supports selecting which columns to show and changing the order of columns.
The ClinVar track can now be filtered to only show ClinVar variants that also appear in gnomAD.