Agent skill

Variant Population Frequency

Query gnomAD for variant allele frequency across populations.

MITAuto-check passed

Install Variant Population Frequency

skills CLI

$ npx skills add InternScience/scp --skill variant-population-frequency -a claude-code

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

GitHub CLI

$ gh skill install InternScience/scp variant-population-frequency --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/InternScience/scp.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/variant-population-frequency .claude/skills/variant-population-frequency && 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/

Paste into Claude Code

Install the "variant-population-frequency" agent skill from https://github.com/InternScience/scp/tree/main/skills/variant-population-frequency into .claude/skills/variant-population-frequency/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "variant-population-frequency", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/InternScience/scp/tree/main/skills/variant-population-frequency

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add InternScience/scp --skill variant-population-frequency -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install InternScience/scp variant-population-frequency --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/variant-population-frequency .agents/skills/variant-population-frequency && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "variant-population-frequency" agent skill from https://github.com/InternScience/scp/tree/main/skills/variant-population-frequency into .agents/skills/variant-population-frequency/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "variant-population-frequency", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add InternScience/scp --skill variant-population-frequency -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install InternScience/scp variant-population-frequency --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/variant-population-frequency .cursor/skills/variant-population-frequency && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "variant-population-frequency" agent skill from https://github.com/InternScience/scp/tree/main/skills/variant-population-frequency into .cursor/skills/variant-population-frequency/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "variant-population-frequency", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/InternScience/scp.git --path skills/variant-population-frequency

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add InternScience/scp --skill variant-population-frequency -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install InternScience/scp variant-population-frequency --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/variant-population-frequency .gemini/skills/variant-population-frequency && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "variant-population-frequency" agent skill from https://github.com/InternScience/scp/tree/main/skills/variant-population-frequency into .gemini/skills/variant-population-frequency/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "variant-population-frequency", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install InternScience/scp variant-population-frequency

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add InternScience/scp --skill variant-population-frequency -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/variant-population-frequency .github/skills/variant-population-frequency && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "variant-population-frequency" agent skill from https://github.com/InternScience/scp/tree/main/skills/variant-population-frequency into .github/skills/variant-population-frequency/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "variant-population-frequency", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add InternScience/scp --skill variant-population-frequency -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install InternScience/scp variant-population-frequency --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/variant-population-frequency .opencode/skills/variant-population-frequency && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "variant-population-frequency" agent skill from https://github.com/InternScience/scp/tree/main/skills/variant-population-frequency into .opencode/skills/variant-population-frequency/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "variant-population-frequency", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: variant-population-frequency
GitHub stars: 169
Used in: 1 other repo
Token cost: ~609 tokens
SKILL.md length: 8 words
Files: 1
Skills in repo: 73
Repo updated: Jun 3, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Query gnomAD for variant allele frequency across populations.

Reaches api.genohub.org and gnomad.broadinstitute.org

What it does

Variant Population Frequency is an agent skill from InternScience/scp. Query gnomAD for variant allele frequency across populations. Uses FAVOR to convert rsID→variantid first, then queries gnomAD.

Its SKILL.md is about 610 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

The licence is MIT.

Example prompts

“/variant-population-frequency”

Requirements

Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit cea5398. 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
No scripts in the folder and no shell commands in SKILL.md (its code samples are tex and python).
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:
- api.genohub.org
- gnomad.broadinstitute.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

Variant Population Frequency loads about 609 tokens when it runs. Until then it costs about 39 tokens; SKILL.md has 8 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~39
When it runs · the whole SKILL.md, loaded when a task matches: ~609

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

The full file from InternScience/scp at commit cea5398, republished under its MIT licence (© InternScience). 8 words, ~609 tokens.

Download SKILL.mdSave it as .claude/skills/variant-population-frequency/SKILL.md (or your agent's skills folder).

name: variant-population-frequency
description: Query gnomAD for variant allele frequency across populations. Uses FAVOR to convert rsID→variant_id first, then queries gnomAD.
license: MIT license
metadata.skill-author: PJLab

gnomAD Population Frequency

Usage

Tool Description

tex

Step 1: Query FAVOR to convert rsID → chr-pos-ref-alt format.
API: GET https://api.genohub.org/v1/rsids/{rs_id}
Step 2: Query gnomAD GraphQL API with the variant_id.
API: POST https://gnomad.broadinstitute.org/api (GraphQL)
Args:
    rs_id (str): dbSNP rsID (e.g. "rs7412")
Return:
    Overall AF, population-specific AF (exome + genome), homozygote counts.

Query Example

python

import requests

rs_id = "rs7412"

# ── Step 1: FAVOR 获取 variant_id (chr-pos-ref-alt) ──
# 注意：FAVOR 可能返回多个变异（多等位基因位点），需遍历所有结果
favor_url = f"https://api.genohub.org/v1/rsids/{rs_id}"
favor_resp = requests.get(favor_url, timeout=30).json()
if not isinstance(favor_resp, list):
    favor_resp = [favor_resp]

variant_ids = [item.get("variant_vcf", "") for item in favor_resp if item.get("variant_vcf")]
print(f"[FAVOR] 该rsID对应 {len(variant_ids)} 个变异: {variant_ids}")

# ── Step 2: gnomAD 查询人群频率（遍历所有变异） ──
query = """
query VariantQuery($variantId: String!) {
  variant(variantId: $variantId, dataset: gnomad_r4) {
    variant_id
    rsid
    exome {
      ac
      an
      af
      ac_hom
      populations { id ac an ac_hom }
    }
    genome {
      ac
      an
      af
      ac_hom
      populations { id ac an ac_hom }
    }
  }
}
"""

for variant_vcf in variant_ids:
    print(f"\n── 查询 {variant_vcf} ──")
    resp = requests.post(
        "https://gnomad.broadinstitute.org/api",
        json={"query": query, "variables": {"variantId": variant_vcf}},
        timeout=30
    ).json()

    v = resp.get("data", {}).get("variant", {})
    if not v:
        print(f"[gnomAD] {variant_vcf}: 未找到数据")
        continue
    print(f"[gnomAD] variant: {v.get('variant_id')}, rsid: {v.get('rsid')}")

    for source in ["exome", "genome"]:
        d = v.get(source, {})
        if d:
            print(f"[gnomAD] {source}: AF={d.get('af')}, AC={d.get('ac')}, AN={d.get('an')}, Hom={d.get('ac_hom')}")
            for pop in (d.get("populations") or []):
                if pop.get("an", 0) > 0:
                    af = pop["ac"] / pop["an"]
                    print(f"  {pop['id']}: AF={af:.6f}, AC={pop['ac']}, AN={pop['an']}")

Files

Just SKILL.md in skills/variant-population-frequency of InternScience/scp.

Open the folder on GitHubat commit cea5398

Used in 2 other repositories

We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in InternScience/scp, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Variant Population Frequency 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.

Variant Population Frequency compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Variant Population Frequency this skillInternScience/scp	169	1 repos	~609	Automated safety check: Pass	MIT	4 mo ago
Bio Clinical Databases Gnomad Frequenciesmajiayu000/claude-skill-registry	666	1 repos	~1.2k	Automated safety check: Pass	MIT	today
Annotating Variantsmaziyarpanahi/openmed	5.5k	—	~2.1k	Automated safety check: Pass	Apache-2.0	today
Bio Population Genetics Scikit Allel AnalysisGPTomics/bioSkills	1.2k	1 repos	~5k	Automated safety check: Pass	MIT	1 mo ago
Bio Clinical Databases Gnomad FrequenciesGPTomics/bioSkills	1.2k	2 repos	~6.2k	Automated safety check: Pass	MIT	1 mo ago
Variant AnnotationClawBio/ClawBio	1.2k	1 repos	~2.8k	Automated safety check: Pass	MIT	today

Similar skills

Bio Clinical Databases Gnomad Frequencies
majiayu000/claude-skill-registry
Query gnomAD for population allele frequencies to assess variant rarity.
666 GitHub starsUsed in 1 repo~1.2k tokens
Auto-check passed
Annotating Variants
maziyarpanahi/openmed
Annotates VCF variants and normalizes HGVS nomenclature with public, license-free annotators (Ensembl VEP REST, VEP/SnpEff/ANNOVAR offline) and links variants to gnomAD population frequencies and…
5.5k GitHub stars~2.1k tokensUpdated today
Research & ScienceAuto-check passed
Bio Population Genetics Scikit Allel Analysis
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In-memory Python population genetics with scikit-allel - GenotypeArray/HaplotypeArray/AlleleCountsArray, diversity (pi, theta, Tajima's D), SFS, FST (Weir-Cockerham, Hudson, Patterson), f3/D…
1.2k GitHub starsUsed in 1 repo~5k tokens
Data & AnalyticsAuto-check passed
Bio Clinical Databases Gnomad Frequencies
GPTomics/bioSkills
Queries gnomAD v4 (807k samples), v3, v2.1.1, and constraint metrics with grpmax FAF95, bottleneck-group exclusion, LOEUF interpretation, SV/CNV/mtDNA catalogs, and Whiffin max-credible-AF framework.
1.2k GitHub starsUsed in 2 repos~6.2k tokens
Research & ScienceAuto-check passed
Variant Annotation
ClawBio/ClawBio
Annotate VCF variants with Ensembl VEP REST, ClinVar significance, gnomAD/population frequency context, and prioritized variant ranking.
1.2k GitHub starsUsed in 1 repo~2.8k tokens
Research & ScienceAuto-check passed
Bio Population Genetics Rare Variant Association
GPTomics/bioSkills
Gene and region-based rare-variant aggregation - burden/collapsing, SKAT, SKAT-O, ACAT-V/ACAT-O, annotation-weighted STAAR - with regenie (--vc-tests), SAIGE-GENE+, and the SKAT R package.
1.2k GitHub starsUsed in 1 repo~4.7k tokens
Research & ScienceAuto-check passed

Questions about Variant Population Frequency

What does Variant Population Frequency do?

Query gnomAD for variant allele frequency across populations. Variant Population Frequency is an agent skill from InternScience/scp. Query gnomAD for variant allele frequency across populations.

How do I install Variant Population Frequency in Claude Code?

Run `npx skills add InternScience/scp --skill variant-population-frequency -a claude-code`. Or copy the skill folder (skills/variant-population-frequency in InternScience/scp) into .claude/skills/variant-population-frequency in your project. Claude Code loads it when a task matches its description.

How do I install Variant Population Frequency in Codex?

Run `npx skills add InternScience/scp --skill variant-population-frequency -a codex`. Or copy the skill folder (skills/variant-population-frequency in InternScience/scp) into .agents/skills/variant-population-frequency in your project. Codex loads it when a task matches its description.

Can I use Variant Population Frequency 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 InternScience/scp --skill variant-population-frequency -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/variant-population-frequency, .gemini/skills/variant-population-frequency, .github/skills/variant-population-frequency and .opencode/skills/variant-population-frequency in your project.

What does Variant Population Frequency need to run?

SKILL.md names no scripts, command-line tools or credentials: Variant Population Frequency is instructions for the agent only. Our summary lists: Python 3.

Does Variant Population Frequency access the network?

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

Is Variant Population Frequency 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 Variant Population Frequency use?

Variant Population Frequency is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Variant Population Frequency use?

About 609 tokens (SKILL.md is roughly 2.4k 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 Variant Population Frequency?

Skills that share tags, products or a category with Variant Population Frequency: Bio Clinical Databases Gnomad Frequencies (majiayu000/claude-skill-registry, 666 stars), Annotating Variants (maziyarpanahi/openmed, 5.5k stars), Bio Population Genetics Scikit Allel Analysis (GPTomics/bioSkills, 1.2k stars) and Bio Clinical Databases Gnomad Frequencies (GPTomics/bioSkills, 1.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Variant Population Frequency?

InternScience (a GitHub organization) maintains it in InternScience/scp, which has 169 GitHub stars. The repository holds 73 skills in this directory. The repository was last updated on June 3, 2026.

Source: InternScience/scp on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Variant Population Frequency

Install Variant Population Frequency

Facts

At a glance

What it does

Example prompts

Requirements

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

gnomAD Population Frequency

Usage

Tool Description

Query Example

Files

Used in 2 other repositories

Compare with similar skills

Similar skills

Bio Clinical Databases Gnomad Frequencies

Annotating Variants

Bio Population Genetics Scikit Allel Analysis

Bio Clinical Databases Gnomad Frequencies

Variant Annotation

Bio Population Genetics Rare Variant Association

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Questions about Variant Population Frequency