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Finding Variants Using dbSNP

This guide introduces the dbSNP database from NCBI and provides a workflow for using it to find variants.

Reasons for Using dbSNP

Common reasons for using dbSNP include:

  • Identifying details about a particular variant (e.g., by searching with an rs number)

  • Finding variants associated with a gene

  • Finding variants with particular features (e.g., clinical significance, function class, minor allele frequency, etc.)

dbSNP's Scope

dbSNP is a database of small scale human variants. dbSNP records include information related to associated publications, population frequency, molecular consequence, and genomic and RefSeq mapping.

Types of Variants in dbSNP

  • Single nucleotide variants

  • Microsatellites

  • Small scale insertions and deletions

  • Common variations and clinical mutations

Reference SNPs

Reference SNPs, also called RefSNPs or rs numbers, are stable, non-redundant identifiers for small-scale variants. RefSNPs are numbers with an "rs" prefix (e.g., rs886055457) and can be directly searched in dbSNP to retrieve variant-level information.

RefSNPs facilitate large-scale studies in association genetics, medical genetics, functional and pharmacogenomics, population genetics and evolutionary biology, personal genomics, and precision medicine.

Additional RefSNP Features

  • Part of globally unique accession series

  • Annotated and linked to the latest human assembly and RefSNP nucleotide and protein sequences

  • Updated to reflect current knowledge of sequence data and biology

  • Continually curated and annotated by NCBI staff and collaborators

  • Searchable across variation and genomic databases

  • Supported and reported in open-source and commercial software and tools

  • Linked to many NCBI internal and external resources, including ClinVar, PubMed, RefSeq, UCSC Genome Browser, EMBL-EBI, TopMed, and GnomAD

Adapted from "About dbSNP Reference (rs) number"