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dbsnp-database

Resolve genetic variants between rsIDs, VCF coordinates, and HGVS via dbSNP.

2.7k|283|Updated May 13, 2026
Search Tags:#genomics#ncbi#dbsnp#hgvs#variant resolution#rsid mapping#vcf coordinates
One-click install
npx skills add https://github.com/google-deepmind/science-skills --skill dbsnp-database-google-deepmind
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: dbsnp-database
Source: https://github.com/google-deepmind/science-skills/tree/main/skills/dbsnp_database
Command: npx skills add https://github.com/google-deepmind/science-skills --skill dbsnp-database-google-deepmind

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This skill helps you identify and interpret short genetic variants by linking rsIDs, genomic coordinates, and HGVS notation to dbSNP records.

Core Features & Use Cases

  • Variant resolution across formats: Convert chromosomal coordinates, VCF-style alleles, or HGVS strings into rsIDs, with automatic GRCh38→GRCh37 fallback.
  • Variant lookup with structured outputs: Retrieve variant type, gene associations, clinical significance labels, minor allele frequencies, and GRCh placements for GRCh38 (or a chosen assembly).
  • Region-based discovery: Search for rsIDs over a specified chromosomal range using NCBI E-utilities and return a controlled number of results to avoid overwhelming payloads.
  • Use case: Given a variant in HGVS (e.g., NC_000008.11:g.19962213del), resolve it to rsID(s), then fetch the rsID record to obtain gene links and allele frequency summaries for downstream analysis.

Quick Start

Use the dbsnp-database skill to resolve a VCF coordinate to rsIDs by asking: uv run scripts/dbsnp_cli.py resolve-variant 8 19962213 C T --output /tmp/resolve.json.

Frequently Asked Questions about dbsnp-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I map VCF coordinates to dbSNP rsIDs?▼

To map VCF coordinates to dbSNP rsIDs, use the dbsnp_cli.py resolve-variant wrapper with chromosome, position, reference, and alternate alleles to retrieve matching dbSNP identifiers and save structured JSON output.

Can I convert HGVS notation to rsIDs for genetic variants?▼

Yes, you can convert HGVS notation to rsIDs by resolving HGVS expressions against dbSNP records. You must quote the HGVS strings in single quotes to ensure safe and accurate variant resolution via the NCBI dbSNP endpoints.

How do I find all rsIDs within a specific chromosomal region?▼

You can find rsIDs within a specific chromosomal region using NCBI E-utilities to search a defined chromosomal range. The process returns a controlled number of results to avoid overwhelming payloads while surveying the region.

Does dbSNP variant resolution support the GRCh37 assembly?▼

Yes, dbSNP variant resolution supports the GRCh37 assembly through an automatic GRCh38 to GRCh37 fallback mechanism, ensuring you can retrieve GRCh placements and variant data even if the primary assembly query fails.

What clinical and frequency data can I retrieve for a resolved rsID?▼

When you retrieve a resolved rsID record, you can obtain variant type, gene associations, clinical significance labels, minor allele frequencies, and GRCh placements for downstream genomic analysis.

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