Gnomad Database

From the author

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).

— the description by Google DeepMind

AutoGineer summary

Written by AutoGineer from the skill’s own files, not by the author

The gnomad-database skill provides a structured interface to query the Genome Aggregation Database (gnomAD). It enables researchers to retrieve allele frequencies for specific genetic variants, obtain gene constraint metrics such as pLI and LOEUF scores, and search for variants within defined genomic regions or genes. The skill includes helper scripts to manage API interactions and rate limits, ensuring consistent data retrieval for genomic analysis.

What it does

Retrieves global and ancestry-specific allele frequencies for genetic variants.
Fetches gene constraint metrics including pLI and LOEUF scores.
Searches for variants within specific genomic regions or genes.
Supports querying by variant ID, rsID, or gene symbol.
Provides filtering allele frequency (FAF) data for variant assessment.

When to use it

When determining the rarity or allele frequency of specific genetic variants.
When assessing loss-of-function intolerance using gene constraint metrics.
When identifying variants located within a particular gene or genomic coordinate range.
When querying structural variants in the context of population genetics.

Advantages

Automated handling of API rate limits via provided helper scripts.
Standardized output formats for variant and gene constraint data.
Integration with local execution environments using managed dependencies.
Direct access to aggregated population-scale genomic data.

Usage examples

“Get the allele frequency for variant 1-55516888-G-GA.”: The agent executes the variant frequency script and returns a JSON file containing global and ancestry-specific allele frequencies for the specified variant.
“What are the constraint metrics for the BRCA1 gene?”: The agent retrieves the pLI and LOEUF scores for BRCA1 and saves the data to a JSON file.
“Find all missense variants in the TP53 gene.”: The agent queries the database for TP53 variants filtered by the missense consequence and outputs the results to a file.

Install

Download the skill as a ZIP:
https://mp-staging.autogineer.com/agent-skills/google-deepmind/gnomad-database/download

Unzip it into the cross-client skills folder of your project:

mkdir -p .agents/skills && unzip gnomad-database.zip -d .agents/skills

Documentation by Google DeepMind

Prerequisites

uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
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

Files

ATTRIBUTION.mdAdded by AutoGineer912 B
LICENSELicence file added by AutoGineer11.1 KiB
SKILL.md3.0 KiB
references/citation.bib5.1 KiB
scripts/get_gene_constraint.pyScript2.4 KiB
scripts/get_variant_frequency.pyScript4.2 KiB
scripts/search_variants.pyScript5.2 KiB

Requirements and compatibility

Works with: Claude Code, Claude apps, OpenAI Codex, GitHub Copilot, Cursor, Gemini CLI, Kiro, OpenCode, Goose, Amp, Roo Code, JetBrains Junie, Factory Droid, Devin (ex-Windsurf), Mistral Vibe, OpenHands, Letta

“Works with” means the tool reads the open Agent Skills format; a skill written for one tool may use features others lack.

Needs: Needs Python

Security

What our scanner noticed· Low risk

Scripts that your agent may run

This skill includes scripts that your agent may run. Read them before you use it.

A static scan is not a guarantee. Skills are third-party content: review a skill before you let an agent use it.

Scvi Tools
K-Dense· Community
A toolkit for fitting probabilistic generative models to single-cell omics data, including RNA, ATAC, and multimodal integration.
Science and researchClaude CodeClaude appsOpenAI Codex+14 more
MITLow riskGitHub stars of the source repository56.4k
Onekgpd
K-Dense· Community
Query individual-level genotype data and variants from the 1000 Genomes Project cohort.
Science and researchClaude CodeClaude appsOpenAI Codex+14 more
MITLow riskHas scriptsGitHub stars of the source repository56.4k
Geniml
K-Dense· Community
A toolkit for managing local genomic interval workflows, including BED validation, consensus universe construction, and model planning.
Science and researchClaude CodeClaude appsOpenAI Codex+14 more
MITLow riskHas scriptsGitHub stars of the source repository56.4k
Latchbio Integration
K-Dense· Community
Develop, register, and operate bioinformatics workflows on the Latch platform using the Python SDK and CLI.
Science and researchClaude CodeClaude appsOpenAI Codex+14 more
MITLow riskHas scriptsGitHub stars of the source repository56.4k
Diffdock
K-Dense· Community
Perform protein-small-molecule docking and pose generation using the DiffDock and DiffDock-L models.
Science and researchClaude CodeClaude appsOpenAI Codex+14 more
MITLow riskHas scriptsGitHub stars of the source repository56.4k
Neuropixels Analysis
K-Dense· Community
End-to-end analysis pipeline for Neuropixels extracellular electrophysiology recordings using SpikeInterface.
Science and researchClaude CodeClaude appsOpenAI Codex+14 more
MITLow riskHas scriptsGitHub stars of the source repository56.4k