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Agent skill

Clinvar Database

by aipoch in aipoch/medical-research-skills

Utilities for querying the NCBI ClinVar database to retrieve variant records, clinical significance, and phenotype relationships; use when searching variants by gene/condition/significance…

MITAuto-check passedResearch & Science

Install Clinvar Database

skills CLI
$ npx skills add aipoch/medical-research-skills --skill clinvar-database -a claude-code

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

GitHub CLI
$ gh skill install aipoch/medical-research-skills clinvar-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/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/'scientific-skills/Evidence Insight/clinvar-database' .claude/skills/clinvar-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
clinvar-database
GitHub stars
2k
Token cost
~856 tokens
SKILL.md length
314 words
Files
6 (incl. scripts, references)
Skills in repo
567
Repo updated
First seen
Licence
MIT

At a glance

Utilities for querying the NCBI ClinVar database to retrieve variant records, clinical significance, and phenotype relationships; use when searching variants by gene/condition/significance…

  • Works in 2 steps: Search ClinVar for pathogenic variants… → Annotate a VCF with ClinVar data
  • Searching variants by gene/condition/significance
  • SKILL.md covers When to Use, Key Features, Dependencies and Example Usage, plus 1 more section
  • Runs Python scripts from its folder; calls python

What it does

Clinvar Database is an agent skill from aipoch/medical-research-skills. Utilities for querying the NCBI ClinVar database to retrieve variant records, clinical significance, and phenotype relationships; use when searching variants by gene/condition/significance, interpreting Pathogenic/Benign/VUS classifications, or annotating VCF files with ClinVar annotations.

Its SKILL.md is about 860 tokens, which your agent loads only when the skill is triggered. The skill folder holds 7 other files, including scripts and reference files (for example `clinvar-database_audit_result_v1.json`, `references/api_reference.md` and `references/clinical_significance.md`).

It sits in Research & Science. It works with NCBI and Python. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.

When your agent uses it

  • Searching variants by gene/condition/significance
  • Interpreting Pathogenic/Benign/VUS classifications
  • Annotating VCF files with ClinVar annotations

Example prompts

  • “Use the clinvar-database skill to utility for querying the NCBI ClinVar database to retrieve variant records, clinical significance, and phenotype…”
  • “/clinvar-database”

Requirements

  • Python 3

Workflow steps

2 steps, taken from the step headings in SKILL.md.

  1. Search ClinVar for pathogenic variants in a gene
  2. Annotate a VCF with ClinVar data

What it can do on your machine

Read from SKILL.md and the folder at commit 686e09d. 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

    Ships 2 files in scripts/ (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python

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

  • Network

    No URLs in SKILL.md.

    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

Clinvar Database loads about 856 tokens when it runs, and up to ~1.1k if it reads all its reference files. Until then it costs about 77 tokens; SKILL.md has 314 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~77
When it runs · the whole SKILL.md, loaded when a task matches
~856
With references · SKILL.md plus every file in references/, read only if the agent opens them
~1.1k

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); the scripts in this folder are not scanned.

SKILL.md

The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 314 words, ~856 tokens.

Download SKILL.mdSave it as .claude/skills/clinvar-database/SKILL.md (or your agent's skills folder). This skill also uses 5 other files; get the full folder from GitHub.
name
clinvar-database
description
Utilities for querying the NCBI ClinVar database to retrieve variant records, clinical significance, and phenotype relationships; use when searching variants by gene/condition/significance, interpreting Pathogenic/Benign/VUS classifications, or annotating VCF files with ClinVar annotations.
license
MIT
author
AIPOCH

Source: https://github.com/aipoch/medical-research-skills

When to Use

  • You need to find ClinVar variant records by gene, condition/phenotype, or clinical significance (e.g., BRCA1 + pathogenic).
  • You want to interpret a variant’s clinical significance (Pathogenic/Benign/VUS) and review status for reporting or triage.
  • You need to annotate a VCF with ClinVar identifiers and interpretation fields as part of a variant annotation pipeline.
  • You want to perform bulk retrieval of ClinVar datasets for offline analysis or periodic database refresh.
  • You are building a workflow that relies on NCBI E-utilities to programmatically query ClinVar.

Key Features

  • ClinVar search via NCBI E-utilities using flexible query terms (gene/condition/significance).
  • Clinical interpretation retrieval, including clinical significance categories and review status.
  • VCF annotation workflow integration (leveraging bcftools) to enrich variants with ClinVar data.
  • Bulk data access through ClinVar FTP downloads for large-scale processing.
  • Reference documentation:
    • API details: references/api_reference.md
    • Clinical significance definitions: references/clinical_significance.md

Dependencies

  • Python >=3.8
  • requests (Python package)
  • bcftools (system dependency; required for VCF annotation)
  • pandas (Python package; optional for downstream data processing)

Example Usage

1) Search ClinVar for pathogenic variants in a gene
bash
python scripts/search.py --term "BRCA1[gene] AND pathogenic[CLNSIG]"
2) Annotate a VCF with ClinVar data
bash
python scripts/annotate.py --input input.vcf --output annotated.vcf

Implementation Details

  • Search (scripts/search.py)

    • Uses NCBI E-utilities to query ClinVar with a user-provided --term.
    • The query term supports ClinVar/Entrez syntax (e.g., BRCA1[gene], pathogenic[CLNSIG]) to filter by gene and clinical significance.
    • Output is expected to include matching ClinVar records/identifiers suitable for follow-up interpretation or annotation.

  • Interpretation fields

    • Clinical significance values (e.g., Pathogenic/Benign/VUS) and related interpretation guidance follow ClinVar conventions; see references/clinical_significance.md.
    • Review status (e.g., level of evidence/review) is retrieved alongside significance where available.

  • VCF annotation (scripts/annotate.py)

    • Takes an input VCF (--input) and produces an annotated VCF (--output).
    • Integrates with bcftools to add ClinVar-derived annotations to variant records (requires bcftools installed and available on PATH).
    • Designed for pipeline use: deterministic input/output files and command-line parameters.

  • Bulk downloads

    • Supports obtaining ClinVar datasets via FTP for offline indexing/annotation workflows.
    • Recommended when you need reproducible, high-throughput annotation without repeated API calls.

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

Files

SKILL.md and 5 other files (scripts, references) in scientific-skills/Evidence Insight/clinvar-database of aipoch/medical-research-skills.

  • SKILL.md
  • clinvar-database_audit_result_v1.json
  • references/api_reference.md
  • references/clinical_significance.md
  • scripts/annotate.py
  • scripts/search.py

Open the folder on GitHubat commit 686e09d

Compare with similar skills

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Biopythonlamm-mit/scienceclaw244—~3.9kAutomated safety check: PassApache-2.0
Bio Biomart QueriesGPTomics/bioSkills1.2k2 repos~3.2kAutomated safety check: PassMIT

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Works with

Categories

Questions about Clinvar Database

What does Clinvar Database do?

Utilities for querying the NCBI ClinVar database to retrieve variant records, clinical significance, and phenotype relationships; use when searching variants by gene/condition/significance…. Clinvar Database is an agent skill from aipoch/medical-research-skills. Utilities for querying the NCBI ClinVar database to retrieve variant records, clinical significance, and phenotype relationships; use when searching variants by gene/condition/significance, interpreting Pathogenic/Benign/VUS classifications, or annotating VCF files with ClinVar annotations.

When should I use Clinvar Database?

Clinvar Database fits situations like: searching variants by gene/condition/significance; interpreting Pathogenic/Benign/VUS classifications; annotating VCF files with ClinVar annotations.

How do I install Clinvar Database in Claude Code?

Run `npx skills add aipoch/medical-research-skills --skill clinvar-database -a claude-code`. Or copy the skill folder (scientific-skills/Evidence Insight/clinvar-database in aipoch/medical-research-skills) into .claude/skills/clinvar-database in your project. Claude Code loads it when a task matches its description.

How do I install Clinvar Database in Codex?

Run `npx skills add aipoch/medical-research-skills --skill clinvar-database -a codex`. Or copy the skill folder (scientific-skills/Evidence Insight/clinvar-database in aipoch/medical-research-skills) into .agents/skills/clinvar-database in your project. Codex loads it when a task matches its description.

Can I use Clinvar 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 aipoch/medical-research-skills --skill clinvar-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/clinvar-database, .gemini/skills/clinvar-database, .github/skills/clinvar-database and .opencode/skills/clinvar-database in your project.

What does Clinvar Database need to run?

Going by SKILL.md and its folder, Clinvar Database needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Clinvar Database access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Clinvar 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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Clinvar Database use?

Clinvar Database 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 Clinvar Database use?

About 856 tokens (SKILL.md is roughly 3.4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 272 tokens, read only when the agent opens those files.

What are the alternatives to Clinvar Database?

Skills that share tags, products or a category with Clinvar Database: ETE Toolkit for Phylogenetic Trees (davila7/claude-code-templates, 32k stars), Biopython (davila7/claude-code-templates, 32k stars), Biopython (K-Dense-AI/scientific-agent-skills, 48k stars) and Biopython (lamm-mit/scienceclaw, 244 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Clinvar Database?

aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,974 GitHub stars. The repository holds 567 skills in this directory. The repository was last updated on September 17, 2026.

Source: aipoch/medical-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.