# Clinvar Database

Use when needing clinical significance, pathogenicity classifications (e.g....

- Repository: https://github.com/google-deepmind/science-skills (3377 stars)
- Category: Engineering
- License: Apache-2.0
- Last updated: 2026-10-23
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add google-deepmind/science-skills --skill clinvar-database -g -a claude-code -y`
Codex: `npx skills add google-deepmind/science-skills --skill clinvar-database -g -a codex -y`
Cursor: `npx skills add google-deepmind/science-skills --skill clinvar-database -g -a cursor -y`
Gemini CLI: `npx skills add google-deepmind/science-skills --skill clinvar-database -g -a gemini-cli -y`

## Description

Use when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls for human genomic variants.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# ClinVar Database

## Prerequisites

1.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
    `uv` is installed and on PATH.
2.  **User Notification**: If .licenses/clinvar_database_LICENSE.txt does not
    already exist in the workspace root directory then (1) prominently notify
    the user to check the terms at https://www.ncbi.nlm.nih.gov/clinvar/, then
    (2) create the file recording the notification text and timestamp.
3.  **`.env` file**: Make sure the `.env` file exists in your home directory.
    Create one if it does not exist.
4.  **`NCBI_API_KEY`** (optional): Raises the NCBI rate limit from 3 to 10
    requests/second. The skill works without it, but a key is recommended if the
    user plans many queries or encounters a 429 error. You can register for a
    key for free at https://www.ncbi.nlm.nih.gov/account/settings/. You **MUST**
    use the safe credentials protocol in the `credentials` skill to check for
    and request this key if this skill looks relevant to the user's request.

## Overview

ClinVar is the primary consensus record for clinical classifications of human
genomic variations. It provides the "clinical ground truth" for pathogenicity
labels (Pathogenic, Likely Pathogenic, Benign, VUS) based on assertions from
global laboratories.

## When to Use

**Use when you need to:**

-   Find the current clinical significance and star rating (review status) for a
    specific variant.
-   Fetch clinician notes, assertion criteria, or rationales for previous
    clinical laboratory classifications.
-   Retrieve the preferred condition name and associated HPO terms for a
    specific variant.
-   Find a list of variant controls (e.g., "Find all Pathogenic variants in the
    HBB gene within 50bp of a signal").
-   Check for conflicting interpretations for a given variant and identify the
    organizations submitting each classification.

**Do NOT use when you need to:**

The rest: https://github.com/google-deepmind/science-skills/blob/HEAD/skills/clinvar_database/SKILL.md