With the gnomAD v4.1 data release, the v4 Pre-Release track has been replaced with the gnomAD v4.1 track. The v4.1 release includes a fix for the allele number issue. The v4.1 track shows variants from 807,162 individuals, including 730,947 exomes and 76,215 genomes. This includes the 76,156 genomes from the gnomAD v3.1.2 release as well as new exome data from 416,555 UK Biobank individuals. For more detailed information on gnomAD v4.1, see the related blog post.

The gnomAD v3.1 track shows variants from 76,156 whole genomes (and no exomes), all mapped to the GRCh38/hg38 reference sequence. 4,454 genomes were added to the number of genomes in the previous v3 release. For more detailed information on gnomAD v3.1, see the related blog post.

The gnomAD v3.1.1 track contains the same underlying data as v3.1, but with minor corrections to the VEP annotations and dbSNP rsIDs. On the UCSC side, we have now included the mitochondrial chromosome data that was released as part of gnomAD v3.1 (but after the UCSC version of the track was released). For more information about gnomAD v3.1.1, please see the related changelog.

GnomAD Genome Mutational Constraint is based on v3.1.2 and is available only on hg38. It shows the reduced variation caused by purifying natural selection. This is similar to negative selection on loss-of-function (LoF) for genes, but can be calculated for non-coding regions too. Positive values are red and reflect stronger mutation constraint (and less variation), indicating higher natural selection pressure in a region. Negative values are green and reflect lower mutation constraint (and more variation), indicating less selection pressure and less functional effect. Briefly, for any 1kbp window in the genome, a model based on trinucleotide sequence context, base-level methylation, and regional genomic features predicts expected number of mutations, and compares this number to the observed number of mutations using a Z-score (see preprint in the Reference section for details). The chrX scores were added as received from the authors, as there are no de novo mutation data available on chrX (for estimating the effects of regional genomic features on mutation rates), they are more speculative than the ones on the autosomes.

The gnomAD Predicted Constraint Metrics track contains metrics of pathogenicity per-gene as predicted for gnomAD v2.1.1 and identifies genes subject to strong selection against various classes of mutation. This includes data on both the gene and transcript level.

The gnomAD v2 tracks show variants from 125,748 exomes and 15,708 whole genomes, all mapped to the GRCh37/hg19 reference sequence and lifted to the GRCh38/hg38 assembly. The data originate from 141,456 unrelated individuals sequenced as part of various population-genetic and disease-specific studies collected by the Genome Aggregation Database (gnomAD), release 2.1.1. Raw data from all studies have been reprocessed through a unified pipeline and jointly variant-called to increase consistency across projects. For more information on the processing pipeline and population annotations, see the following blog post and the 2.1.1 README.

gnomAD v2 data are based on the GRCh37/hg19 assembly. These tracks display the GRCh38/hg38 lift-over provided by gnomAD on their downloads site.

On hg38 only, a subtrack "Gnomad mutational constraint" aka "Genome non-coding constraint of haploinsufficient variation (Gnocchi)" captures the depletion of variation caused by purifying natural selection. This is similar to negative selection on loss-of-function (LoF) for genes, but can be calculated for non-coding regions, too. Briefly, for any 1kbp window in the genome, a model based on trinucleotide sequence context, base-level methylation, and regional genomic features predicts expected number of mutations, and compares this number to the observed number of mutations using a Z-score (see Chen et al 2024 in the Reference section for details). The chrX scores were added as received from the authors, as there are no mutations available for chrX, they are more speculative than the ones on the autosomes.

For questions on the gnomAD data, also see the gnomAD FAQ.

More details on the Variant type(s) can be found on the Sequence Ontology page.

To view the full description, click here.

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