Examples
Worked examples
- Is an instance
A bioinformatics pipeline outputs a VCF file of variant calls from a new sequencing run; before further analysis, each call is annotated with its dbSNP rs ID (if one already exists) so downstream tools and collaborators can refer to the exact same variant unambiguously across studies.
- Is an instance
A researcher designing a genotyping array cross-references candidate SNP positions against dbSNP to confirm each one is a previously catalogued, validated variant rather than a sequencing artifact unique to a single study.
Counter-examples
Looks similar, but isn't
- Not an instance
A variant reported only in a single unpublished lab notebook, never submitted to dbSNP by any submitter, has no rs number and cannot be looked up in dbSNP -- inclusion requires an actual submission to the database, not just genuine existence in someone's raw data.
Editorial commentary
dbSNP (the Single Nucleotide Polymorphism Database) is a public archive operated by the National Center for Biotechnology Information (NCBI) that catalogues short genetic variation — single nucleotide polymorphisms, small insertions and deletions, and other short variants — within and across species, though the human variant set dominates its use. It was initiated in 1998 through a collaboration between NCBI and the National Human Genome Research Institute (NHGRI), making it one of the oldest continuously operated genomic databases still in active use.
What a dbSNP entry actually is
Every distinct short variant submitted to dbSNP — by a sequencing consortium, a genotyping-array manufacturer, or an individual research group — is assigned a persistent Reference SNP (rs) identifier (e.g. rs429358). That identifier tracks the variant’s genomic position and alleles, letting researchers, clinicians, and software tools refer to the exact same variant unambiguously across studies, papers, and databases, regardless of which reference genome build a given analysis used. dbSNP is deliberately agnostic about clinical significance or how common a variant is — it records that a variant exists and where, nothing more.
How dbSNP relates to ClinVar and gnomAD
dbSNP is frequently the first of three related NCBI/partner resources a researcher encounters, and it is worth distinguishing them explicitly. dbSNP answers “does this variant exist, and what is its stable identifier.” ClinVar answers “what clinical significance has been asserted for this variant by submitting laboratories.” gnomAD answers “how common is this variant across large reference populations.” A single rs-numbered variant commonly has both a ClinVar interpretation and a gnomAD frequency attached to it in downstream annotation pipelines, but dbSNP itself carries neither.
Scope and what dbSNP does not hold
Larger structural variants are handled by a companion resource, the Database of Genomic Structural Variation (DGVa), rather than dbSNP itself — for example, the 1000 Genomes Project submitted its catalogued SNPs and short indels to dbSNP, while its longer structural variant calls went to DGVa. dbSNP also does not hold raw sequencing reads (that is the role of the Sequence Read Archive) or aggregate frequency statistics beyond what individual submitters choose to report alongside their variant submissions.
Examples
- A bioinformatics pipeline outputs a VCF file of variant calls from a new sequencing run; before further analysis, each call is annotated with its dbSNP rs ID (if one already exists) so downstream tools and collaborators can refer to the exact same variant unambiguously across studies.
- A researcher designing a genotyping array cross-references candidate SNP positions against dbSNP to confirm each one is a previously catalogued, validated variant rather than a sequencing artifact unique to a single study.
Counter-example
A variant reported only in a single unpublished lab notebook, never submitted to dbSNP by any submitter, has no rs number and cannot be looked up in dbSNP — inclusion requires an actual submission to the database, not just genuine existence in someone’s raw data.
Related infrastructure
See also ClinVar for clinical variant interpretation, gnomAD for population allele frequencies, and the 1000 Genomes Project, one of dbSNP’s major historical variant-submission sources.
Machine-readable encodings
Use in your systems
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