dbSNP celebrates 20 years!


dbSNP was established in August 1999 as a collaboration between NCBI and the National Human Genome Research Institute (NHGRI) as a database of small scale nucleotide variants. The database includes both common and rare single-base nucleotide variation (SNV), short (=< 50bp) deletion/insertion polymorphisms, and other classes of small genetic variations.

Since 1999, dbSNP has grown exponentially in size, has thousands of users worldwide, and makes measurable impacts in the fields of large-scale studies in association genetics, medical genetics, functional and pharmaco-genomics, population genetics, and evolutionary biology. Today, dbSNP is an authoritative and trusted central repository for human variations. At dbSNP, we archive, curate, and annotate submissions on all classes of simple molecular variation, including neutral polymorphisms as well as those that cause rare clinical phenotypes.

dbSNP offers researchers and clinicians the ability to mine over half a billion non-redundant and uniquely accessioned Reference SNP (RefSNP) records generated from nearly two billion records from thousands of submitters. We annotate RefSNPs on all latest genomic assemblies and Reference Sequences  (mRNA, Protein, and RefSeqGene). RefSNP records include variation data (alleles, genotypes, frequency), clinical assertions through ClinVar, molecular consequences, and publications. Over 145 thousand RefSNP accessions have been cited in 50 thousand publications. These identifiers continue to serve as a common method for reporting variants and their effects.

dbSNP data are the basis of scientific variant resources such as ClinVar, OMIM, SNPedia, the Variant Annotation Integrator at UCSC, and the Variant Effect Predictor at EBI.  dbSNP data are also the backbone for variant discovery and analysis platforms, SNP array design, and popular genetic ancestry, health and trait reporting services.

We offer these data without restrictions, through multiple channels and in multiple formats. On the web you can search for data, retrieve a record or browse data across the human genome assembly in the Variation Viewer. You can access the FTP site to download the data in JSON and VCF formats. We also have an specialized API for retrieving individual records in JSON format, example:

https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/328

We have recently modernized the dbSNP build system using NCBI remapping, new variation notation (SPDI), and the Variant Overprecision Correction Algorithm (VOCA).  The system provides a more precise RefSNP mapping, clustering, and variant normalization. To learn how you can use our Variation Services to normalize, remap, and annotate your variants, see our webinar recording on this topic. Try it yourself for a single HGVS expression of your choice.

 

 

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