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Agent skill

Gnomad Database

by jaechang-hits in jaechang-hits/SciAgent-Skills

gnomAD v4 population variant frequencies via GraphQL API. An agent skill from jaechang-hits/SciAgent-Skills.

Custom licenceAuto-check passedResearch & Science

Install Gnomad Database

skills CLI
$ npx skills add jaechang-hits/SciAgent-Skills --skill gnomad-database -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install jaechang-hits/SciAgent-Skills gnomad-database --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/genomics-bioinformatics/databases/gnomad-database .claude/skills/gnomad-database && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
gnomad-database
GitHub stars
371
Used in
1 other repo
Token cost
~7.2k tokens
SKILL.md length
1,175 words
Files
1
Skills in repo
169
Repo updated
First seen
Licence
Custom licence

At a glance

gnomAD v4 population variant frequencies via GraphQL API. An agent skill from jaechang-hits/SciAgent-Skills.

  • Works in 5 steps: Use gnomad_r4 for GRCh38 analyses:… → Use faf95.popmax for clinical filtering,… → Add time.sleep(0.5) in batch loops:… → …
  • Tasks that involve Bioinformatics
  • SKILL.md covers Overview, When to Use, Prerequisites and Quick Start, plus 9 more sections
  • Calls pip; reaches gnomad.broadinstitute.org

What it does

Gnomad Database is an agent skill from jaechang-hits/SciAgent-Skills. gnomAD v4 population variant frequencies via GraphQL API. Allele counts and frequencies stratified by ancestry (AFR, AMR, EAS, NFE, SAS, FIN, ASJ, MID), gene-level constraint (pLI, LOEUF, missense z), and coverage. Identify rare or constrained variants. For clinical pathogenicity use clinvar-database; for GWAS use gwas-database.

Its SKILL.md is about 7.2k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Bioinformatics and GraphQL. It works with GraphQL. The repository describes itself as: 197 bioinformatics & life science skills for Claude Code and AI agents — BixBench 92.0% accuracy. RNA-seq, single-cell, drug discovery, proteomics, and more. Powers OmicsHorizon.

When your agent uses it

  • Tasks that involve Bioinformatics
  • Tasks that involve GraphQL

Example prompts

  • “/gnomad-database”

Requirements

  • Python 3

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

  1. Use gnomad_r4 for GRCh38 analyses: gnomAD v4 is the most current dataset with 730K+ individuals. Use gnomad_r2_1 only when comparing to…
  2. Use faf95.popmax for clinical filtering, not overall AF: The filtering allele frequency accounts for maximum population stratification and…
  3. Add time.sleep(0.5) in batch loops: gnomAD has no published rate limits but the API is shared infrastructure. Polite delays prevent…
  4. Filter lof == "HC" for LoF burden analyses: Low-confidence LoF ("LC") annotations are often in repetitive regions or may be sequencing…
  5. Check AN before interpreting AF: Low allele number (AN) means poor coverage in that population. A zero or near-zero AF may reflect absent…

What it can do on your machine

Read from SKILL.md and the folder at commit 82c862c. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Shell commands in SKILL.md call:

    • pip

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Hosts in commands or code, which the agent is likely to contact:

    • gnomad.broadinstitute.org

    Also links to:

    • doi.org

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Gnomad Database loads about 7.2k tokens when it runs. Until then it costs about 87 tokens; SKILL.md has 1,175 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~87
When it runs · the whole SKILL.md, loaded when a task matches
~7.2k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 1,175 words (~7,153 tokens).

“The Genome Aggregation Database (gnomAD) is a resource of aggregated exome and genome sequencing data from 730,000+ individuals. It provides population variant frequencies stratified by 9 ancestry groups, gene-level constraint scores (pLI, LOEUF), and read coverage information. Access is free…”

— opening of SKILL.md by jaechang-hits, Custom licence
name
gnomad-database
license
ODbL-1.0

Read the full SKILL.md on GitHub

Files

Just SKILL.md in skills/genomics-bioinformatics/databases/gnomad-database of jaechang-hits/SciAgent-Skills.

Open the folder on GitHubat commit 82c862c

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in jaechang-hits/SciAgent-Skills, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Gnomad Database next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Gnomad Database compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Gnomad Database this skilljaechang-hits/SciAgent-Skills3711 repos~7.2kAutomated safety check: PassCustom licence
Encode Ccres Databasegoogle-deepmind/science-skills3.2k1 repos~1.7kAutomated safety check: PassApache-2.0
Gnomad DatabaseLeonChaoX/qinyan-academic-skills9431 repos~3.1kAutomated safety check: PassCC0-1.0
Knowledge Graph ToolsDrugClaw/DrugClaw125—~1.7kAutomated safety check: PassApache-2.0
Nodejs Backend Patternsever-works/ever-works16218 repos~4kAutomated safety check: PassAGPL-3.0
API DesignerJeffallan/claude-skills12k1 repos~2kAutomated safety check: PassMIT

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Works with

Categories

Questions about Gnomad Database

What does Gnomad Database do?

gnomAD v4 population variant frequencies via GraphQL API. An agent skill from jaechang-hits/SciAgent-Skills. Gnomad Database is an agent skill from jaechang-hits/SciAgent-Skills. gnomAD v4 population variant frequencies via GraphQL API.

When should I use Gnomad Database?

Gnomad Database fits situations like: tasks that involve Bioinformatics; tasks that involve GraphQL.

How do I install Gnomad Database in Claude Code?

Run `npx skills add jaechang-hits/SciAgent-Skills --skill gnomad-database -a claude-code`. Or copy the skill folder (skills/genomics-bioinformatics/databases/gnomad-database in jaechang-hits/SciAgent-Skills) into .claude/skills/gnomad-database in your project. Claude Code loads it when a task matches its description.

How do I install Gnomad Database in Codex?

Run `npx skills add jaechang-hits/SciAgent-Skills --skill gnomad-database -a codex`. Or copy the skill folder (skills/genomics-bioinformatics/databases/gnomad-database in jaechang-hits/SciAgent-Skills) into .agents/skills/gnomad-database in your project. Codex loads it when a task matches its description.

Can I use Gnomad Database in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add jaechang-hits/SciAgent-Skills --skill gnomad-database -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/gnomad-database, .gemini/skills/gnomad-database, .github/skills/gnomad-database and .opencode/skills/gnomad-database in your project.

What does Gnomad Database need to run?

Going by SKILL.md and its folder, Gnomad Database needs the command-line tools its instructions call (pip). Our summary lists: Python 3.

Does Gnomad Database access the network?

SKILL.md names 2 domains. In commands or code: gnomad.broadinstitute.org; the agent is likely to contact it when it follows the instructions. As links in the text: doi.org. This is read from the text; nothing was executed.

Is Gnomad Database safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Gnomad Database use?

Gnomad Database has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.

How many tokens does Gnomad Database use?

About 7.2k tokens (SKILL.md is roughly 29k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Gnomad Database?

Skills that share tags, products or a category with Gnomad Database: Encode Ccres Database (google-deepmind/science-skills, 3.2k stars), Gnomad Database (LeonChaoX/qinyan-academic-skills, 943 stars), Knowledge Graph Tools (DrugClaw/DrugClaw, 125 stars) and Nodejs Backend Patterns (ever-works/ever-works, 162 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Gnomad Database?

jaechang-hits (a GitHub user) maintains it in jaechang-hits/SciAgent-Skills, which has 371 GitHub stars. The repository holds 169 skills in this directory. The repository was last updated on September 29, 2026.

Source: jaechang-hits/SciAgent-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.