How do I install the Gnomad Database skill?

Run npx skillmds add phoroth/gnomad-database in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Gnomad Database safe to use?

This skill has not completed SkillMD's automated safety review yet. Capability flags: executes scripts, makes network calls. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Gnomad Database?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Gnomad Database free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Gnomad Database?

phoroth (@phoroth) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Gnomad Database by phoroth — Agent Skill

Name: Gnomad Database
Rating: 4.2 (5 reviews)
Author: phoroth

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).

phoroth badd58e 5 files · 20.0 KB Updated Sep 8, 2026 3 repo stars

File contents

gnomAD Database

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

---name: gnomad-databasedescription: 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).---# gnomAD Database## Prerequisites1. **`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 ScriptsAll scripts are located in the `scripts/` subdirectory of this skill'sinstallation directory. When running them, use the full absolute path to thescript (e.g. `/path/to/gnomad_database/scripts/get_variant_frequency.py`).**1. Variant Frequency.** Retrieves global and ancestry-specific allelefrequencies, homozygote counts, and **Grpmax Filtering AF** (faf95/faf99) forexome, genome, and total (exome+genome combined) data. The filtering allelefrequency (FAF) is the maximum credible genetic ancestry group AF (lower boundof 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`.```bash# 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 responsewill explicitly contain `pli`, and the LOEUF score is represented by`oe_lof_upper`.```bashuv 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.```bash# 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```## ReferencesFurther documentation on the data: https://gnomad.broadinstitute.org/data#apiMore general database documentation: https://gnomad.broadinstitute.org/help

Frequently asked questions