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Protocols

dbSNP specifications

Information


Unique identifier OMICS_00264
Name dbSNP
Alternative name database of Short Genetic Variations
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainers


  • person_outline dbSNP
  • person_outline Stephen Sherry

Additional information


https://www.ncbi.nlm.nih.gov/books/NBK174586/

Publications for database of Short Genetic Variations

dbSNP citations

 (2335)
library_books

Mutations in six nephrosis genes delineate a pathogenic pathway amenable to treatment

2018
Nat Commun
PMCID: 5958119
PMID: 29773874
DOI: 10.1038/s41467-018-04193-w

[…] Sequence reads were mapped against the human reference genome (NCBI build 37/hg19) using CLC Genomics Workbench (version 6.5.1) software (CLC bio). Variants with minor allele frequencies <1% in the dbSNP (Version 137) database were selected and annotated for impact on the encoded protein and for conservation of the reference base and amino acid among orthologs across phylogeny. Mutation calling […]

call_split

Case Report: Identification of an HNF1B p.Arg527Gln mutation in a Maltese patient with atypical early onset diabetes and diabetic nephropathy

2018
PMCID: 5952643
PMID: 29764441
DOI: 10.1186/s12902-018-0257-z
call_split See protocol

[…] h uses a Bayesian genotype likelihood model to report alleles and Phred-scaled confidence values []. Variants (SNVs and indels) were called with SAMTools, with reference to public databases including dbSNP and 1000Genomes and gnomAD []. Analysis was performed with preference to variants located in genes implicated in atypical non-autoimmune forms of diabetes and early-onset obesity. The prioritize […]

call_split

Molecular, Pathological, Radiological, and Immune Profiling of Non brainstem Pediatric High Grade Glioma from the HERBY Phase II Randomized Trial

2018
Cancer Cell
PMCID: 5956280
PMID: 29763623
DOI: 10.1016/j.ccell.2018.04.004
call_split See protocol

[…] ct Predictor v74 (ensembl.org/info/docs/variation/vep) incorporating SIFT (sift.jcvi.org) and PolyPhen (genetics.bwh.harvard.edu/pph2) predictions, COSMIC v64 (sanger.ac.uk/ genetics/CGP/cosmic/) and dbSNP build 137 (ncbi.nlm.nih.gov/sites/SNP) annotations. Copy number was obtained by calculating log2 ratios of tumor/normal coverage binned into exons of known Ensembl genes, smoothed using circular […]

library_books

A case report of heterozygous TINF2 gene mutation associated with pulmonary fibrosis in a patient with dyskeratosis congenita

2018
PMCID: 5959423
PMID: 29742735
DOI: 10.1097/MD.0000000000010724

[…] nome GRCh37/hg19 assembly using the BWA software and analyzed by the Picard-tools-1.118, GATK.v4, and SnpEff_v4.1.software.[–] The mean depth of target regions was 141X. Variants were annotated using dbSNP142, 1000 Genome, ESP, ClinVar, and our in-house database. Finally, candidate pathogenic variants identified by WES were verified with Sanger sequencing.Three-dimensional structures’ templates of […]

library_books

Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine based chemotherapy

2018
BMC Cancer
PMCID: 5948914
PMID: 29751792
DOI: 10.1186/s12885-018-4471-x

[…] e second criteria), there were 17 common SNPs predicted to be either “probably” or “possibly damaging” (Additional file : Table S2). For the SIFT analysis (i.e. the third criteria), we used the “SIFT dbSNP batch tool” to retrieve prediction results for all common nsSNPs and found that only 9 of them were predicted as “Deleterious” with the SIFT score equal to or less than 0.05 (Additional file : T […]

library_books

Genomic features of renal cell carcinoma with venous tumor thrombus

2018
Sci Rep
PMCID: 5945671
PMID: 29748622
DOI: 10.1038/s41598-018-25544-z

[…] c SNVs were called functional, when they were nonsynonymous, occurred within splice sites, or lead to gain or loss of stop codons. All SNVs were annotated using Annovar (version as of February 2016), dbSNP (build 147), 1000 Genomes and EVS (Exome Variant Server, NHLBI GO Exome Sequencing Project (ESP), Seattle, WA [version ESP6500SI-V2]) data. Indels were identified with Platypus callVariants (ver […]

Citations

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dbSNP institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA; National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
dbSNP funding source(s)
Supported by an appointment to the NLM Associate Fellowship Program.

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