Agent skill · research science · google-deepmind
clinvar-database
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.
Why this skill is useful
Provides domain-specific knowledge on querying the ClinVar database for genomic variant classifications that the AI wouldn't reliably generate on its own.
What it needs
Requires uv installed locally. Requires ncbi account access. About 8k tokens when loaded. Last updated 2026-07-07. 2,648 stars on the source repository.
What this skill does
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/clinvardatabaseLICENSE.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. NCBIAPIKEY (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: Find specific allele frequencies in global populations (use gnomAD). Describe the normal biological role of a protein and typical inheritance patterns (use OMIM). …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills google-deepmind/clinvar_database