dbSNP Database

Overview

NCBI dbSNP is the primary public repository for short human genetic variants, cataloguing over 1 billion SNPs, indels, and MNVs with allele frequencies, functional annotations, and cross-references to ClinVar, gnomAD, and 1000 Genomes. Variants are identified by stable rsIDs (reference SNP cluster IDs). Access is free via two APIs: the legacy NCBI E-utilities and the newer NCBI Variation Services REST API, which returns structured JSON.

When to Use

• Looking up allele frequencies and variant class for a known rsID
• Searching all dbSNP variants in a gene or chromosomal region by name or coordinates
• Resolving rsIDs to genomic coordinates (GRCh38/GRCh37) and HGVS notation
• Checking whether a variant of interest has clinical significance links to ClinVar entries
• Batch-fetching hundreds of rsIDs efficiently using epost+efetch history server
• Cross-referencing a list of variant positions to dbSNP rsIDs for downstream annotation
• For clinical pathogenicity classifications use clinvar-database; dbSNP provides IDs and frequency but not curated clinical significance
• For population frequency stratified by ancestry use gnomad-database; dbSNP MAF is a single aggregate frequency

Prerequisites