Agent skill · research science · google-deepmind
gnomad-database
Query the Genome Aggregation Database (gnomAD). Use when determining the rarity or allele frequency of specific genetic variants, retrieving gene constraint metrics (pLI, LOEUF) to assess loss-of-function intolerance, finding variants in a genomic region or gene, or querying structural variants. Don't use for analyzing individual patient genomes, tracking somatic mutations in cancer (use COSMIC), or requesting raw sequencing reads (use ENA).
Why this skill is useful
Adds executable scripts for querying the gnomAD database, providing specific allele frequency and gene constraint metrics that the AI wouldn't generate on its own.
What it needs
Requires uv installed locally. About 2k tokens when loaded. Last updated 2026-07-07. 2,648 stars on the source repository.
What this skill does
gnomAD Database Prerequisites 1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH. 2. User Notification: If .licenses/gnomaddatabaseLICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://gnomad.broadinstitute.org/policies and https://gnomad.broadinstitute.org/data#api, then (2) create the file recording the notification text and timestamp. Core Rules Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the gnomAD API rate limits gracefully. Notification: If this skill is used, ensure this is mentioned in the output. Utility Scripts All scripts are located in the scripts/ subdirectory of this skill's installation directory. When running them, use the full absolute path to the script (e.g. /path/to/gnomaddatabase/scripts/getvariantfrequency.py). 1. Variant Frequency. Retrieves global and ancestry-specific allele frequencies, homozygote counts, and Grpmax Filtering AF (faf95/faf99) for exome, genome, and total (exome+genome combined) data. The filtering allele frequency (FAF) is the maximum credible genetic ancestry group AF (lower bound of the 95% or 99% CI). Variant ID format must be chrom-pos-ref-alt (e.g., 1-55516888-G-GA). Alternately, you may provide an rsID. 2. Gene Constraint. Retrieves constraint metrics for a gene. The response will explicitly contain pli, and the LOEUF score is represented by oelofupper. 3. Region/Gene Variant Search. Finds all variants in a region or gene. References Further documentation on the data: https://gnomad.broadinstitute.org/data#api More general database documentation: https://gnomad.broadinstitute.org/help
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills google-deepmind/gnomad_database