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Agent skill

Variant Clinical Significance

by InternScience in InternScience/scp

Query NCBI ClinVar for variant clinical pathogenicity classification (Pathogenic/Benign/VUS), review status and associated diseases.

MITAuto-check passedResearch & Science

Install Variant Clinical Significance

skills CLI
$ npx skills add InternScience/scp --skill variant-clinical-significance -a claude-code

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

GitHub CLI
$ gh skill install InternScience/scp variant-clinical-significance --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-clinical-significance .claude/skills/variant-clinical-significance && 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
variant-clinical-significance
GitHub stars
170
Used in
1 other repo
Token cost
~348 tokens
SKILL.md length
8 words
Files
1
Skills in repo
73
Repo updated
First seen
Licence
MIT

At a glance

Query NCBI ClinVar for variant clinical pathogenicity classification (Pathogenic/Benign/VUS), review status and associated diseases.

  • Research & Science work in your project
  • Reaches api.ncbi.nlm.nih.gov

What it does

Variant Clinical Significance is an agent skill from InternScience/scp. Query NCBI ClinVar for variant clinical pathogenicity classification (Pathogenic/Benign/VUS), review status and associated diseases.

Its SKILL.md is about 350 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. It works with NCBI. The licence is MIT.

When your agent uses it

  • Research & Science work in your project

Example prompts

  • “/variant-clinical-significance”

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.ncbi.nlm.nih.gov

    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 Clinical Significance loads about 348 tokens when it runs. Until then it costs about 41 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
~41
When it runs · the whole SKILL.md, loaded when a task matches
~348

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, ~348 tokens.

Download SKILL.mdSave it as .claude/skills/variant-clinical-significance/SKILL.md (or your agent's skills folder).
name
variant-clinical-significance
description
Query NCBI ClinVar for variant clinical pathogenicity classification (Pathogenic/Benign/VUS), review status and associated diseases.
license
MIT license
metadata.skill-author
PJLab

ClinVar Clinical Significance

Usage

Tool Description
tex
Query dbSNP refsnp API to extract ClinVar RCV clinical records for a variant.
API: GET https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/{rsid_number}
Args:
    rs_id (str): dbSNP rsID (e.g. "rs7412")
Return:
    ClinVar RCV records: clinical significance (Pathogenic/Benign/VUS/drug-response etc.),
    review status, associated diseases, accession numbers.
Query Example
python
import requests

rs_id = "rs7412"

# 通过 rsID 查询 dbSNP，提取 ClinVar RCV 记录
rsid_num = rs_id.replace("rs", "")
url = f"https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/{rsid_num}"
resp = requests.get(url, timeout=30).json()
snapshot = resp.get("primary_snapshot_data", {})

for ann in snapshot.get("allele_annotations", []):
    for clin in ann.get("clinical", []):
        accession = clin.get("accession_version", "")
        diseases = clin.get("disease_names", [])
        significances = clin.get("clinical_significances", [])
        review = clin.get("review_status", "")
        print(f"[ClinVar RCV] {accession}: {significances}, diseases={diseases}, review={review}")

© InternScience, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in skills/variant-clinical-significance 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 Clinical Significance 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 Clinical Significance compared with similar skills
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Variant Clinical Significance this skillInternScience/scp1701 repos~348Automated safety check: PassMIT
Dbsnp Databasegoogle-deepmind/science-skills3.2k2 repos~3.4kAutomated safety check: NotesApache-2.0
Biopython Bioinformaticsaiming-lab/AutoResearchClaw15k—~810Automated safety check: PassMIT
Bio Write SequencesGPTomics/bioSkills1.2k3 repos~2.1kAutomated safety check: PassMIT
Mako Loreliebaojun/MakoCode155—~692Automated safety check: PassCustom licence
PubMed REST API Searchdavila7/claude-code-templates33k14 repos~3.9kAutomated safety check: PassMIT

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Works with

Categories

Questions about Variant Clinical Significance

What does Variant Clinical Significance do?

Query NCBI ClinVar for variant clinical pathogenicity classification (Pathogenic/Benign/VUS), review status and associated diseases. Variant Clinical Significance is an agent skill from InternScience/scp. Query NCBI ClinVar for variant clinical pathogenicity classification (Pathogenic/Benign/VUS), review status and associated diseases.

When should I use Variant Clinical Significance?

Variant Clinical Significance fits situations like: research & Science work in your project.

How do I install Variant Clinical Significance in Claude Code?

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

How do I install Variant Clinical Significance in Codex?

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

Can I use Variant Clinical Significance 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-clinical-significance -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-clinical-significance, .gemini/skills/variant-clinical-significance, .github/skills/variant-clinical-significance and .opencode/skills/variant-clinical-significance in your project.

What does Variant Clinical Significance need to run?

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

Does Variant Clinical Significance access the network?

SKILL.md names 1 domain. In commands or code: api.ncbi.nlm.nih.gov; the agent is likely to contact it when it follows the instructions. This is read from the text; nothing was executed.

Is Variant Clinical Significance 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 Clinical Significance use?

Variant Clinical Significance 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 Clinical Significance use?

About 348 tokens (SKILL.md is roughly 1.4k 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 Clinical Significance?

Skills that share tags, products or a category with Variant Clinical Significance: Dbsnp Database (google-deepmind/science-skills, 3.2k stars), Biopython Bioinformatics (aiming-lab/AutoResearchClaw, 15k stars), Bio Write Sequences (GPTomics/bioSkills, 1.2k stars) and Mako Lore (liebaojun/MakoCode, 155 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Variant Clinical Significance?

InternScience (a GitHub organization) maintains it in InternScience/scp, which has 170 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.