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Gnomad Database skill

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).

$npx skills add google-deepmind/science-skills --skill gnomad-database
GitHub stars
3,445
Pack installs
91k
Alyn Score
68/99
Updated
5 h ago
License
Apache-2.0

Google DeepMind

Gnomad Database

Backend Science Research

Install Gnomad Database

Pick your agent. Every command is ready to paste.

$npx skills add google-deepmind/science-skills --skill gnomad-database

The open skills CLI detects your agents (Claude Code, Cursor, Codex and 70+ more) and installs to the right folder. Add -g to install globally.

01

Install it

Run the command above, or upload the folder in Claude.

02

Ask naturally

Describe the task. Your agent loads gnomad-database when the request matches its description.

03

Name it if needed

If it does not trigger, say “use the gnomad-database skill”. In Codex, type $gnomad-database.

The skill itself

SKILL.md

GitHub

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/gnomad_database_LICENSE.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/gnomad_database/scripts/get_variant_frequency.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.

# By variant ID:
uv run scripts/get_variant_frequency.py --variant_id {variant_id} [--dataset {dataset}] --output variant_frequency.json

# By rsID (e.g., rs1800562):
uv run scripts/get_variant_frequency.py --rsid {rsid} [--dataset {dataset}] --output variant_frequency.json

2. Gene Constraint. Retrieves constraint metrics for a gene. The response will explicitly contain pli, and the LOEUF score is represented by oe_lof_upper.

uv run scripts/get_gene_constraint.py --gene {gene_symbol} --output {gene_symbol}_constraint.json

3. Region/Gene Variant Search. Finds all variants in a region or gene.

# By region:
uv run scripts/search_variants.py --chrom {chrom} --start {start} --end {end} --output region_variants.json
# By gene:
uv run scripts/search_variants.py --gene {gene_symbol} --consequence {pLoF|missense} --output {gene_symbol}_variants.json

References

Further documentation on the data: https://gnomad.broadinstitute.org/data#api More general database documentation: https://gnomad.broadinstitute.org/help

Tips for Gnomad Database

  • • Start a fresh session after installing so your agent picks up the new skill.
  • • This skill ships scripts. Read them before the first run, and run it in a project without secrets first.
  • • It bundles reference files. The agent reads them only when needed, so they cost no context until then.
  • • It is part of a pack with 40 skills. Install only the ones you need with --skill to keep triggers precise.
  • • If two skills overlap, mention the one you want by name.

Questions about Gnomad Database

What does the Gnomad Database skill do?

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).

How do I install Gnomad Database?

Run "npx skills add google-deepmind/science-skills --skill gnomad-database" in your project. The skills CLI installs it for Claude Code, Cursor, Codex and 70+ other agents. In Claude on the web, upload the skill folder as a ZIP under Customize > Skills.

Does Gnomad Database work in Cursor and Codex?

Yes. Gnomad Database uses the open SKILL.md format, so it works in Claude Code, Claude, Cursor, OpenAI Codex, Gemini CLI, GitHub Copilot and other agents that support agent skills.

Is Gnomad Database free?

Gnomad Database is open source on GitHub under the Apache-2.0 license. It is free to install; check the license before commercial use.

Who made Gnomad Database?

Gnomad Database is published by Google DeepMind in the google-deepmind/science-skills repository, together with 39 other skills.

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