gnomAD changelog

Loss-of-Function Curations in gnomAD v4

Fri, 03 Oct 2025 00:00:00 GMT

The gnomAD v4 dataset now includes loss-of-function (LoF) curations as part of the variant data viewable on the gene, region, and variant pages. We will continue to update the gnomAD browser as additional v4 curations are performed.

See the data page to download the raw data, and the help page and blog post on loss-of-function curations for additional details.

Deprecation of gnomAD Data on Azure Open Datasets

Tue, 22 Jul 2025 00:00:00 GMT

Starting August 15, 2025, gnomAD data will no longer be accessible via Azure Open Datasets due to Microsoft Azure’s planned deprecation of genomic datasets.

Users who have been relying on Azure Open Datasets for gnomAD data access should transition to accessing data in Google Cloud Public Datasets or the Registry of Open Data on AWS. For more information on how to access gnomAD downloadable data, see our Data page.

Release v4.1 CNV and SV browser tables

Fri, 18 Apr 2025 00:00:00 GMT

We have released two Hail Tables underlying the browser display of the gnomAD v4.1 copy number variant (CNV) and structural variant (SV) data.

Two additional tables are now available: We have released two new tables in addition to the three tables released last summer:

gnomAD v4.1 CNV Hail Table
gnomAD v4.1 SV Hail Table

For more information about these tables, please refer to our help text on the browser release tables.

To download these tables, visit our downloads page.

De novo variants from gnomAD v4.1 exomes

Thu, 20 Mar 2025 00:00:00 GMT

To expand the number of publicly available control de novo variants, we have released 1,953 coding de novo variants (DNVs) called from 1,517 trios in the gnomAD v4.1 exomes.

We generated these calls by adapting Hail’s hl.de_novo method and Kaitlin Samocha’s de novo caller. We filtered variants to include only variants that were outside low-confidence regions, did not have a * alt allele, passed variant QC, had coding consequences, and passed gnomAD v4.1 exomes allele frequency and callset allele count filters. We additionally filtered to keep only variants with high and medium confidence of being true de novos, which resulted in a high-quality set of 1,953 coding DNVs. The observed de novo mutation rate per proband (~1.29 per exome) aligns with expected rates (Kaplanis & Samocha et al., Nature 2020).

We are continuing to refine our approach by integrating parent-specific de novo priors and better adjustments for false homozygous reference genotypes in the proband. We hope to release an updated dataset soon.

For more details on our de novo detection methods, visit our gnomad_qc GitHub repository and gnomad_methods GitHub repository.

To download the DNV dataset, visit our downloads page.

Update known disease-associated tandem repeat (TR) pages

Thu, 20 Mar 2025 00:00:00 GMT

We have updated the gnomAD TR pages. Changes include:

Adding 9 recently discovered disease-associated TR loci
Introducing a “Color by” feature to the allele size histograms which allows users to see basic genotype quality scores derived from either manual review of read visualizations or from ExpansionHunter confidence intervals
Removing all PCR-plus samples and samples with 100bp reads

Loci

We added these 9 recently discovered disease-associated TR loci:
RILPL1, THAP11, ZFHX3, FGF14, ABCD3, NAXE, PRE-MIR7-2, FAM193B, and EP400.

We also added 9 other TR loci, including NOTCH2NLA, FRA10AC1, and TMEM185A, which, to our knowledge, are not currently linked to rare diseases, but have historically appeared in various STR catalogs as suspected disease-causing loci.

The updated dataset now includes a total of 77 TR loci.

Samples

We also updated the TR callset to remove 732 samples that had 100bp read lengths. All remaining samples have 150bp reads. We also removed all PCR-plus samples. We then added 626 PCR-free genome samples from the Human Genome Diversity Project (HGDP). The updated dataset now has genotypes from 16,328 genomes for 73 of the loci, and from 14,035 genomes for 4 loci (NAXE, PRE-MIR7-2, FAM193B, and EP400) with the difference being due to changes in cloud access to read data.

Genotype Quality Scores

We added two genotype quality scores: Q and ManualReviewGenotypeQuality.

The Q score ranges between 0 (low quality) and 1 (high quality) and is based on the ratio between the allele size and the width of the confidence interval reported by ExpansionHunter. It is described in more detail in [Jam 2023] and is evaluated in [Weisburd 2023].

The ManualReviewGenotypeQuality is available for 4,819 out of 1,411,171 (0.3%) genotypes, and is based on manual review of read visualizations. To select which genotypes to review for each locus, we started with the longest alleles at the tail of the allele size distribution and then reviewed progressively shorter alleles either until we reached a natural stopping point, or until we had reviewed over 100 genotypes for that locus. We looked for informative image features described in [Dolzhenko 2022] and our previous blog post and recorded the genotype quality as:

High - if the genotype appears to be accurate
Medium - if the genotype is probably accurate, but there are indications that it might be wrong by 3 or more repeats
Low - if the genotype is probably wrong by 3 or more repeats

For most loci, two people reviewed the genotypes, and the average of their responses was taken as the final genotype quality.

User Interface

The user interface now includes a new “Color by” selector under the allele size histogram, enabling a color overlay based on genotype quality scores or other annotations. Then, in addition to “Linear” and “Log” options in the y-Scale selector, users can now choose “Linear: truncated” to more easily see the tail of the distribution. The External Resources section now includes a link to STRchive - a new website that provides up-to-date information on pathogenic thresholds, phenotypes, ages of onset, and other important aspects of known disease-associated loci. Finally, the Read Data section includes new options and metadata related to the genotype quality scores.

Downloads

The updated Downloads table (which contains 1 row for each TR genotype) has several new columns. ManualReviewGenotypeQuality and Q columns contain the newly-added genotype qualities, while the PublicProjectId and PublicSampleId columns contain the source project and individual ids (example: “Human Genome Diversity Project” and “HGDP01400”) for 3,102 samples from the HGDP and 1000 Genomes projects.

Update gnomAD browser gene model Hail Tables

Thu, 16 Jan 2025 00:00:00 GMT

The gnomAD browser gene model Hail Tables that were previously released have been updated. The tables have been repartitioned from 2,000 to 100 partitions, this smaller amount of paritions is more appropriate for the size of these tables, which should improve efficiency when using them in computations. Futher, the GRCh38 gene model table now includes GTEx and pext data, and the structure of the GTEx and pext data has changed from the previous struct, to an array.

For more information about these tables, please refer to our help text on the browser release tables.

To download these tables, visit our downloads page.

Proportion expressed across transcripts (pext) on gnomAD v4.1

Fri, 22 Nov 2024 00:00:00 GMT

Updated transcript tissue expression and proportion expressed across transcripts (pext) tracks have been added to the gene pages in the gnomAD v4 browser.

The updated tracks in the gnomAD v4 browser were generated using GTEx v10 bulk tissue transcript expression data.

The previous versions of these tracks, available in the gnomAD v2 browser, were generated using GTEx v7. For more information about the proportion expressed across transcripts (pext) score, including its utility and how it is generated, please see our help page.

Release gnomAD browser tables

Thu, 29 Aug 2024 00:00:00 GMT

The Hail Tables that underlie the gnomAD browser are now available for public use. These tables closely mirror the structure of the browser, enabling users familiar with the gene and variant pages to easily access the full set of underlying data in a format consistent with the browser’s organization.

For more information about these tables, please refer to our help text on the browser release tables.

To download these tables, visit our downloads page.

Three tables are now available:

gnomAD v4.1 browser variants Hail Table
GRCh38 browser gene models Hail Table
GRCh37 browser gene models Hail Table

browser variants Hail Table

The browser variant table consolidates data from the gnomAD exome, genome, and joint frequency releases into a single, unified table. Frequency information is stored as a dictionary, and the key-value pairs allow for easy access to specific frequencies.

GRCh38/GRCh37 Gene Models Hail Tables

The gene models tables aggregate relevant information from multiple sources into a single table. For each gene, data is included from GENCODE, HGNC, and MANE transcripts. Information from GTEx, and various gnomAD secondary analyses are available in the GRCh37 table but are not yet available in the GRCh38 table.

gnomAD v4.1 updates

Thu, 02 May 2024 00:00:00 GMT

This changelog entry discusses smaller updates to gnomAD added with the v4.1 release that were not discussed in the blog post.

As part of gnomAD v4.1, we have added the following new features:

Browser display of non-UK Biobank (non-UKB) subset of gnomAD v4 exomes
Supplementary files containing REVEL scores for variants in 2,414 transcripts that weren’t scored in the v4.0 release
New joint exome + genome frequency resources with statistical tests flagging variants with discrepant frequencies

We have also updated the following features:

Gene constraint metrics
Exome copy number variants
Genome structural variants
Stats page

Browser display of non-UK Biobank subset

As part of gnomAD v4.1, we have exposed the non-UK Biobank (non-UKB) subset of the gnomAD v4 exomes. This subset was previously only available in our downloadable files but is now available in the “Dataset” toggle on gene, transcript, region, and variant pages. Note that this subset only impacts variant frequencies in the exomes; none of the genome samples were from the UK Biobank. Therefore, when the non-UKB subset is selected, the exome variant frequencies will update to reflect counts from the non-UKB subset, and the genome numbers will remain unchanged.

Example variant:

Supplementary REVEL files

We used a combination of transcript information (MANE Select or canonical) from Ensembl v105 and variant information (locus and alleles combination) to ascertain REVEL scores for variants in gnomAD v4.0 and v4.1 (exomes and genomes). However, REVEL was computed using Ensembl v64. This means that variants within 2,414 MANE Select transcripts in gnomAD v4.0 and v4.1 are missing REVEL scores because they were present in Ensembl v105 but not in Ensembl v64.

To address this, we annotated the variants within the 2,414 genes with the maximum REVEL score found at the specific locus and allele, rather than the score for the MANE Select or canonical transcript. We have released two TSVs; the exomes TSV adds REVEL scores to 1,936,321 out of 2,284,296 (87.77%) missense variants within the 2,414 genes. The genomes TSV adds REVEL scores to 528,204 out of 620,799 (85.08%) missense variants within the 2,414 genes.

Joint frequency VCFs

We have released a downloadable Hail Table and VCFs containing statistical tests that flag variants with discordant frequencies in the gnomAD exomes and genomes. For more information about these tests, please see our blog post and help page.

Gene constraint metrics

We regenerated the gene constraint metrics using gnomAD v4.1 frequencies and have updated the constraint table on the gene and transcript pages. Note that these updated metrics have the same caveats as the v4.0 metrics; for more details, please see our blog post.

Exome copy number variants

The exome copy number variants (CNVs) have been updated to include:

Variant 193076__DUP relabeled as 16p12.2_DUP
Refined annotation of 15q11 and 22q11 loci
Updated N_EXN_VAR and N_INT_VAR labels for size of events to be consistent with the genic annotation used by short variant team
Updated sex karyotype terminology (“XX” and “XY” instead of “Male” and “Female”)
SC (site count), SN (site number), and SF (site frequency) labels reformatted to match the short variant VCF format (e.g., updating “afr_SC” to “SC_afr”)

Genome structural variants

The genome structural variants (SVs) have been updated to include:

Genotype information for multiallelic CNVs (mCNVs)
Updated genetic ancestry (e.g., “Other” to “Remaining”) and sex karyotype terminology (same as CNVs above)
Updated gene annotations (using the same gene list used for the short variants)
Updated metric annotation order to match the short variant VCF format (e.g., updating “nfe_AF” to “AF_nfe”)

Fix gene page variant table export to csv

Fri, 01 Dec 2023 00:00:00 GMT

The CSV file containing the information in the variant table for a given gene has been corrected to display the proper counts for each genetic ancestry group.

Any user utilizing a CSV file generated from a v4 gene page should re-download the CSV file to ensure they have the correct data.

On the gene page, users can download the information present in the variant table to a CSV file for local usage. With the release of v4, this CSV file contained faulty counts for AC, AN, AF, and Number of Homozygotes for certain genetic ancestry groups. When adding up the exome and genome counts for a given variant, differing indexes of genetic ancestry groups in a list resulted in the browser incorrectly combining counts for different groups.

This has now been corrected, and any v4 variants CSV file downloaded before this was patched (Dec 01, 2023) should be re-downloaded.

Fixed chromosome Y VCF for v4.0 exomes

Thu, 16 Nov 2023 00:00:00 GMT

The exome chromsome Y VCF that was originally released on November 1st, 2023 was a duplicate of the genome chromosome Y VCF. The duplicate has been replaced by the correct VCF as November 16th, 2023.

Regional Missense Constraint Metric in gnomAD

Wed, 01 Nov 2023 00:00:00 GMT

The regional missense constraint (RMC) track has now been added to the gene pages in the gnomAD v2 browser.

This track was previously only available on the ExAC browser and has been updated to include three distinct views:

Genes that exhibit evidence of regional variability in missense intolerance will have regional missense constraint information displayed
Genes that were searched for but that did not exhibit any evidence of regional differences in missense intolerance will have transcript-wide missense constraint information displayed
Outlier genes will have text indicating that these genes were not searched for regional differences in missense intolerance

Note that regional missense constraint was only calculated on canonical transcripts (single canonical transcript per gene).

The updated track has a new color scheme to more clearly visualize regions of missense intolerance and a more detailed hover-over to provide more information about each domain of regional missense constraint.

For more information about how these data were generated, please see the RMC help page.

The location of the RMC track

Filter ClinVar Variants by review status

Fri, 22 Sep 2023 00:00:00 GMT

The ClinVar variants track now includes an option to filter by review status. ClinVar assigns a review status to each variant, along with a corresponding number of gold stars, ranging from 0 to 4 stars.

Users will now be able to filter ClinVar variants based on review status by selecting one of the following options from a dropdown: 0-4 Stars, >=1 Stars, >=2 Stars, >=3 Stars, 4 Stars.

Displaying neighboring variants when searching the variant table

Mon, 18 Sep 2023 00:00:00 GMT

Previously, performing a search in the Variant table would remove all neighboring rows from view, leaving only the exact search results displayed. This often resulted in a loss of context regarding a variant’s position in the table and its surrounding variants.

Now, there is an option to enable the display of nearby variants. When “Display neighboring variants” is selected, users are able to search for specific variants and also view nearby variants in the table. As users search, the table automatically jumps to the first search result, which is highlighted.

Searching the variant table without enabling “Display neighboring variants”.

Searching the variant table enabling “Display neighboring variants”.

Population frequency display modified

Thu, 24 Aug 2023 00:00:00 GMT

Previously, for a given population, when a variant had an allele number (AN) of 0, the Allele Frequency (AF) in the population frequencies table would be displayed as 0. This was misleading, as it implied understanding of the frequency of the variant, where there was none.

Now, in those cases, the AF is now displayed as a ’-’ character. This helps users distinguish at a glance when there is no frequency information known about a variant for a given population or subpopulation.

ClinVar track bugfixes

Thu, 17 Aug 2023 00:00:00 GMT

The ClinVar track on Gene pages had several bugs that were identified and fixed, resulting in a more stable and accurate experience for users.

Previously, several circumstances would cause the ClinVar variants plot to crash when clicking the “expand to all variants” button. Several edge cases and off-by-one errors that had existed in the logic to render this plot have been fixed, resulting in a more stable experience. Further, an edge case on reverse strand genes incorrectly caused some frameshift variants to render in the opposite direction and as the entire length of the gene, this has been fixed leading to a plot that accurately depicts these frameshift variants.

Genome build added to dropdown menus

Tue, 15 Aug 2023 00:00:00 GMT

Previously, when selecting a gnomAD variant dataset in the search bar or in the dataset selection dropdown, the dataset’s reference genome version was not displayed.

With this change, the reference genome version (GRCh37 or GRCh38) is now visible next to the gnomAD variant dataset version, making it more clear to users which dataset to select.

The search bar

The dataset selection dropdown

Modify navigation bar links

Fri, 11 Aug 2023 00:00:00 GMT

The ordering of the links on the navigation bar has been updated to reflect the frequency of their usage. The order of the links is now: About, Team, Policies, Publications, Blog, Changelog, Downloads, Help/FAQ.

In addition, the link formerly titled “News” is now “Blog”, and the link formerly titled “Help” is now titled “Help/FAQ”.

Update variant interpretation paper

Mon, 31 Jul 2023 00:00:00 GMT

The link to the variant interpretation paper on the home page has been updated to a more recent publication.

Fix co-occurrence table rendering on v3 datasets

Tue, 18 Jul 2023 00:00:00 GMT

Previously, the variant co-occurrence table on the gene page incorrectly rendered on v3 datasets. This was unintentional and misleading, as the analysis was not performed on v3.

Now, the co-occurrence table only renders on v2 datasets, as intended.

Update contact page

Tue, 18 Jul 2023 00:00:00 GMT

The contact page (previously the feedback page) has had its contents updated for clarity.

Add All of Us link on variant page

Mon, 17 Jul 2023 00:00:00 GMT

A link to the All of Us (AoU) data browser has been added to the variant pages under the “External resources” section. This lets users quickly navigate to the same variant on the AoU data browser.

Change gene search results sorting

Mon, 10 Jul 2023 00:00:00 GMT

Previously, when a user searched for a gene, a gene that had an alternate symbol that closely matched the search term could appear first in the list of suggested gene symbols. This led to confusing behavior and the need to pay close attention to which results the search bar returned.

Now, any gene with a canonical symbol that matches the search term is prioritized in the list of search results. This results in an overall more intuitive user experience when searching for genes by symbol.

As an example, the search term ABCD previously would result in the gene CX3CL1 as the first search result, as ABCD-3 is an alternate symbol for CX3CL1. With this change, searching for ABCD now results in ABCD1 as the first search result, as it prioritizes canonical gene symbols.

Update to Elasticsearch 7

Tue, 20 Jun 2023 00:00:00 GMT

The gnomAD browser’s backend database has had a major version update applied. It is now running Elasticsearch 7 and was previously running Elasticsearch 6. This update has been tested thoroughly and should represent no change in functionality or service.

Update team page

Mon, 22 May 2023 00:00:00 GMT

The team page has been updated to reflect changes in gnomAD staff and council.

Update GraphQL API to TypeScript

Fri, 19 May 2023 00:00:00 GMT

The gnomAD browser’s public GraphQL API has had its language updated to TypeScript, from JavaScript. This update has been tested thoroughly and should represent no change in functionality or service.

Update publications page

Fri, 17 Mar 2023 00:00:00 GMT

The publications page has been updated to include a more up to date list of publications, as well as to update the citation format to denote which authors contributed equally.

With the update of the publications page, the citations topic on the help page has been removed. The citations topic URL now redirects to the updated publications page.

Add gene page link on variant page

Fri, 17 Mar 2023 00:00:00 GMT

Previously, users that wanted to go to the corresponding gene page, from a variant page, would scroll down to the “Variant Effect Predictor” section of the variant page, and click on one of the gene links. In cases where many distinct variant pages were open, users expressed interest in a more direct way to go to the gene page.

With this change, a button labeled “Gene” has been added to the header row of a variant page where there is a single canonical transcript. This button allows users to quickly navigate to the gene that the variant falls in. In the rare case where there is no single canonical transcript, there is no gene page button, and users should instead use the Variant Effect Predictor section.

In order to accomodate the extra button, the phrase Single Nucleotide Variant has been abbreviated to SNV on the corresponding variant pages.

Add favicon

Wed, 08 Mar 2023 00:00:00 GMT

A favicon has been added to the gnomAD browser. This will help users to distinguish which tabs are gnomAD at a glance. The favicon is styled like the coverage plot, showing coverage for both exomes and genomes.

Update downloads page

Wed, 15 Feb 2023 00:00:00 GMT

The gnomAD Downloads Page has been redesigned to make it easier to explore datasets released by the gnomAD production team and gnomAD-affiliated research groups.

Previously, our major releases (gnomAD v2, gnomAD v3, and ExAC) were organized under tabs that users would click to see which datasets were available for each release. This tab-based navigation scheme made it difficult to quickly understand the information hierarchy on the page. It also prevented users from searching the page using the standard internet browser search functionality (CTRL + F).

Now, instead of tabs, the new layout features a table of contents on the righthand side. Users will have a better sense of what is available and can quickly jump to specific releases and datasets. To help maintain a sense of context, the table of contents synchronizes with the page position as the user scrolls. Since all text is on the same page, CTRL-F searching is now possible.

Furthermore, the new Downloads Page attempts to distinguish which datasets are produced by the gnomAD production team (“Core Dataset”) from downstream analyses carried out by affiliated research groups (“Secondary Analyses”). For example, our recently released Genomic Constraint analysis falls into the latter category.

Fix OS variant table flag display

Thu, 02 Feb 2023 00:00:00 GMT

Previously, if a variant had an Other Splice loss of function flag as a consequence, the variant table would incorrectly display both a Low Confidence flag (LC pLoF), as well as the Other Splice flag (OS pLoF).

Now, in those cases, table only displays the Other Splice flag.

Update team page

Mon, 30 Jan 2023 00:00:00 GMT

The team page has been updated to include headshots and bios for gnomAD staff members.

Monoallelic flag added to variant table

Wed, 30 Nov 2022 00:00:00 GMT

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

Tue, 09 Aug 2022 00:00:00 GMT

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

Tue, 09 Aug 2022 00:00:00 GMT

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

Wed, 15 Dec 2021 00:00:00 GMT

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.

Zooming in on PCSK9

To zoom in, click the “Zoom in” button above the coverage track. Select a region of the gene or transcript to zoom in on using the start and stop inputs or the slider. When zoomed in, a “mini-map” will display which region of the gene or transcript is currently visible. To view a different region, click “Select different regions” or adjust the slider. To zoom out and see the full gene or transcript, click the “View full gene” or “View full transcript” button.

Coverage added to variant pages

Fri, 22 Oct 2021 00:00:00 GMT

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.

gnomAD v3.1.2

Fri, 22 Oct 2021 00:00:00 GMT

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

Fri, 22 Oct 2021 00:00:00 GMT

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.

MANE transcripts updated to release 0.95

Fri, 22 Oct 2021 00:00:00 GMT

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.

In addition, an issue has been fixed that, in some cases, resulted in a gene’s MANE Clinical Plus transcript being displayed as its MANE Select transcript.

Navigate directly to structural variants

Fri, 03 Sep 2021 00:00:00 GMT

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.

Dataset options for search

Population frequencies table moved to the top of the variant page

Thu, 19 Aug 2021 00:00:00 GMT

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

Tue, 17 Aug 2021 00:00:00 GMT

Detailed information about ClinVar variants, such as submissions, is now available in the ClinVar variants track on gene, region, and transcript pages.

ClinVar variants track

When the ClinVar variants track is expanded, hovering the pointer over a variant shows some information about the variant. Previously, clicking on a variant would navigate to the ClinVar website.

ClinVar variant details

Now, clicking on a variant shows additional information, such as submissions, without leaving the gnomAD browser.

Changes to transcript tissue expression visualization

Mon, 16 Aug 2021 00:00:00 GMT

To help identify biologically relevant transcripts, the gene page includes information from the GTEx project on transcripts’ expression in different tissues.

Previous transcript tissue expression visualization

Previously, this was displayed next to transcripts in the transcripts track. However, only one tissue could be selected at a time and the x-axis was scaled based on the selected tissue, making it difficult to compare expression across tissues.

Current transcript tissue expression visualization

Now, the transcripts track shows a dot next to each transcript, the size of which is scaled based on that transcript’s mean expression across all tissues. This maintains the ability to find the most expressed transcript(s) at a glance. Hovering the pointer over the dot shows the transcript’s mean expression across all tissues as well as the tissue in which the transcript is most expressed.

Heatmap of transcript tissue expression

Information on expression in specific tissues can be seen by pressing the “Show transcript tissue expression” button. This brings up a heatmap that displays expression for all transcripts in all tissues.

Transcript expression added to pext track

Mon, 16 Aug 2021 00:00:00 GMT

Transcript tissue expression information from the GTEx project has been added to the individual tissue pext tracks.

Expanding the pext track on the gene page shows which exonic regions are expressed in each tissue. However, since the y-axis of each track is normalized 0 to 1, it does not show which tissues the gene is expressed in. That information is available in the transcripts track.

Transcript tissue expression in the pext track

Now, the pext track shows a dot next to each tissue, the size of which is scaled based on the mean expression in that tissue across all the gene’s transcripts. Hovering the pointer over the dot shows the mean expression in that tissue across all transcripts as well as the transcript most expressed in that tissue.

The individual tissue pext tracks can also now be sorted by the mean transcript expression in the tissue.

Variant co-occurrence (phasing) information added

Thu, 12 Aug 2021 00:00:00 GMT

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

Mon, 09 Aug 2021 00:00:00 GMT

We recently removed all gnomAD VCFs from our public buckets, as these files are now hosted via public dataset programs on three major cloud providers. We have now moved all remaining public gnomAD data to a requester-pays bucket and plan to make these files free to access through public dataset programs soon.

Until then, users will need to change the root bucket for public gnomAD files from gs://gnomad-public to gs://gnomad-public-requester-pays; the filepaths otherwise remain the same. For more information on accessing data in requester-pays buckets, see our previous announcement.

Rename filter in mitochondria dataset and minor format changes

Tue, 03 Aug 2021 00:00:00 GMT

We corrected:
1. dbSNP rsIDs. The dbSNP resource we used to annotate rsIDs was not split for multi-allelic variants, so if a variant was multi-allelic in the dbSNP b154 VCF, this variant received no rsID annotation. This has been fixed in the release Hail Table and VCFs. When adding this fix we noticed that some variants can have multiple rsIDs associated with them, so we now store rsID as a set instead of a string in the release Hail Table.
We changed:
1. The name of the “heteroplasmy_below_10_percent” filter to “heteroplasmy_below_min_het_threshold” to maintain consistency in the filter name while allowing for flexibility in changes to the value of the threshold in the future.
2. The header of the VCF for “indel_stack” to specify heteroplasmic variants.
We added:
1. A global annotation (“global_annotation_description”) that contains the descriptions for annotations found in the Hail Table.

gnomAD VCFs removed from public bucket

Thu, 08 Jul 2021 00:00:00 GMT

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.

For many months, the download links for VCFs on our browser have pointed to copies hosted by our cloud partners, so users won’t experience any disruption or notice any differences when they navigate to the browser to download gnomAD data. Users who were previously accessing VCF files by browsing our public bucket will need to change the bucket from which they pull files. These buckets are listed at https://gnomad.broadinstitute.org/downloads.

Liftover

Tue, 27 Apr 2021 00:00:00 GMT

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.

For variants in v2, but not in v3, there will be a link to take you to a 40 base region centered on the lifted over locus.

gnomAD v3.1.1

Sat, 20 Mar 2021 00:00:00 GMT

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).

We corrected:

VEP annotations. There was an issue in gnomAD v3.1 in which some variants were missing VEP annotations. This release fixes the missing annotations in the Hail Tables and VCFs.
The score chosen for in silico predictors. Some variants have multiple scores for one or more of the in-silico predictors, based on additional information provided by each in-silico predictor, such as trinucleotide context and transcript, that is not listed on the gnomAD browser. In the v3.1 release, the score annotated on the release Hail Table was not standardized. We decided in the v3.1.1 release to keep only the highest score for each in-silico predictor and add an additional has_duplicate annotation to the in-silico predictor structs in the release Hail Table for each score to indicate whether a variant had multiple scores. This is also flagged on the variant pages of the browser.
dbSNP rsIDs. The dbSNP resource we used to annotate rsIDs was not split for multi-allelic variants, so if a variant was multi-allelic in the dbSNP b154 VCF, this variant received no rsID annotation. This has been fixed in the release Hail Table and VCFs. When adding this fix we noticed that some variants can have multiple rsIDs associated with them, so we now store rsID as a set instead of a string in the release Hail Table.
VCF headers. VEP version, dbSNP version, and age distributions information in the VCF header were changed to match VCF specifications.

We changed:

The format of missing subset frequency info in the release Hail Table. Previously, if a variant was not observed in a subset, the frequency struct in the freq annotation was set to {AC: 0, AF: 0.0, AN: Null, homozygote_count: 0}. For this release we modified this to store all entries in the struct as missing.
VCF release files to use underscore field separators instead of hyphens for the INFO fields. Hyphenated info keys are not allowed in version 4.3 of the VCF specification (item 8 of section 1.6.1), current gnomAD VCFs are on version 4.2.

We added:

A global annotation to the release Hail Table freq_sample_count that includes the sample counts for each element of the allele frequency freq array.
The AS_SB_TABLE field to the release VCFs, which was already present in the release Hail table.

New help page

Wed, 10 Mar 2021 00:00:00 GMT

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

Tue, 09 Mar 2021 00:00:00 GMT

The ClinVar track can now be filtered by VEP consequence category (pLoF, missense / inframe indel, synonymous, other) as well as pathogenicity.

MANE Select / Ensembl canonical transcripts noted on transcript pages

Mon, 08 Mar 2021 00:00:00 GMT

Transcript pages now note if the transcript is the MANE Select or Ensembl canonical transcript for its gene.

For example, ENST00000302118:

Change to population labels

Mon, 08 Mar 2021 00:00:00 GMT

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 for mitochondrial variants

Thu, 18 Feb 2021 00:00:00 GMT

Population frequencies are now available for mitochondrial variants.

Configure variant table columns

Tue, 16 Feb 2021 00:00:00 GMT

The variant table now supports selecting which columns to show and changing the order of columns.

Columns are now available to show:

dbSNP rsID
HGVS coding sequence
HGVS protein sequence
base-level pext score

Filter ClinVar track to variants in gnomAD

Fri, 12 Feb 2021 00:00:00 GMT

The ClinVar track can now be filtered to only show ClinVar variants that also appear in gnomAD.