# Dbsnp Database

Use when you want to look up, map, and search for short genetic variants (SNPs, indels)...

- Repository: https://github.com/google-deepmind/science-skills (3377 stars)
- Category: Data and ML
- 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 dbsnp-database -g -a claude-code -y`
Codex: `npx skills add google-deepmind/science-skills --skill dbsnp-database -g -a codex -y`
Cursor: `npx skills add google-deepmind/science-skills --skill dbsnp-database -g -a cursor -y`
Gemini CLI: `npx skills add google-deepmind/science-skills --skill dbsnp-database -g -a gemini-cli -y`

## Description

Use when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database. Resolves between rsIDs, genomic coordinates in VCF format, and HGVS strings. For an rsID, returns variant type, gene associations, clinical significance, allele frequencies, and genomic coordinates (GRCh38).

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

# dbSNP Database Integration

## 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/dbsnp_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/snp/, 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.

## Core Rules

-   **Use the Wrapper**: ALWAYS execute the provided wrapper script
    `scripts/dbsnp_cli.py` to query the database rather than constructing custom
    HTTP or curl requests. The script automatically handles rate limiting,
    retries, and JSON parsing.
-   **Command Choice**: Do NOT use `search-region` to find the rsID of a
    specific variant; use `resolve-variant` instead.
-   **Output Size**: Avoid using `--full` on `get-variant` unless specifically
    needed, as raw payloads can exceed 1 MB.
-   **Shell Safety**: Always wrap HGVS strings in single quotes to prevent shell
    expansion errors.
-   **Notification**: If this skill is used, ensure this is mentioned in the
    output.

## When to Use

**Use this skill when you need to:**

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