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Review
. 2025 Jan 6;53(D1):D925-D931.
doi: 10.1093/nar/gkae977.

The evolution of dbSNP: 25 years of impact in genomic research

Lon Phan  1 , Hua Zhang  1 , Qiang Wang  1 , Ricardo Villamarin  1 , Tim Hefferon  1 , Aravinthan Ramanathan  1 , Brandi Kattman  1
Affiliations
Review

The evolution of dbSNP: 25 years of impact in genomic research

Lon Phan et al. Nucleic Acids Res. .

Abstract

The Single Nucleotide Polymorphism Database (dbSNP), established in 1998 by the National Center for Biotechnology Information (NCBI), has been a critical resource in genomics for cataloging small genetic variations. Originally focused on single nucleotide polymorphisms (SNPs), dbSNP has since expanded to include a variety of genetic variants, playing a key role in genome-wide association studies (GWAS), population genetics, pharmacogenomics, and cancer research. Over 25 years, dbSNP has grown to include more than 4.4 billion submitted SNPs and 1.1 billion unique reference SNPs, providing essential data for identifying disease-related genetic variants and studying human diversity. Integrating large-scale projects like 1000 Genomes, gnomAD, TOPMed, and ALFA has expanded dbSNP's catalog of human genetic variation, increasing its usefulness for research and clinical applications. Keeping up with advancements such as next-generation sequencing and cloud-based infrastructure, dbSNP remains a cornerstone of genetic research supporting continued discoveries in precision medicine and population genomics. DATABASE URL: https://www.ncbi.nlm.nih.gov/snp.

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Figures

Graphical Abstract
Graphical Abstract
Figure 1.
Figure 1.
Timeline of dbSNP milestones and genomics submissions. This timeline categorizes key events in dbSNP history and related genomics submissions. Notably, the completion of the Human Genome Project in 2003 significantly increased dbSNP submissions. ‘Events’ include the establishment of dbSNP in 1998, reaching 1 million RS in 2000, the 2017 redesign and the 25th anniversary in 2024. ‘Submissions’ feature significant contributions like HapMap (2004), 1000 Genomes (2009), ExAC (2015), GnomAD (2017) and TopMed (2020) (13–17). The figure illustrates the chronological order and importance of these milestones.
Figure 2.
Figure 2.
Growth of dbSNP Submitted SNP (ss) and Reference SNP (rs) accessions over time. The growth of dbSNP records over time, highlighting the increase in both Submitted SNP (ss) and Reference SNP (rs) accessions. As observed, there was steady growth in the number of Submitted SNP (ss) accessions starting around 2005, with a significant acceleration in growth following the completion of the human genome in 2003 (Figure 1) and after 2010, driven by advances in sequencing technologies and major genomic projects. While the number of submitted SNPs (ss) continues to grow, the plateau of rs accessions after 2020 reflects variants based on GRCh38 genome assembly, though additional unknown variants may still be discovered through the Telomere-to-Telomere (T2T) genome and pangenome projects.
Figure 3.
Figure 3.
Gene locus, RNA and coding sequence (CDS) feature locations used for assignment of consequences and SO terms. This figure illustrates the locations of key gene features, including gene loci, RNA transcripts and coding sequences (CDS), used by dbSNP to assign functional consequences and Sequence Ontology (SO) terms to genetic variants. By mapping variants to specific locations within the gene, dbSNP classifies them into categories such as synonymous, missense, frameshift or splice site variants.
Figure 4.
Figure 4.
dbSNP RefSNP page for rs268, illustrating the layout and key sections of the redesigned interface. The page includes allele frequency data, clinical significance, and functional consequences for the selected rs. The ALFA Allele Frequency section provides aggregated allele frequency data from global populations, as shown by the specific sub-populations (e.g. European, African, East Asian, etc.). Further details and explanations of each tab and section are available in the Supplementary File (Supplementary Figure S1).
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