Variation

The Variation database provides human genomic variation retrieval. Original data source of Variation database includes dbSNP, dbVar, ClinVar, etc. The main available information includes genome variation(HGVS), location, organism, population frequency, related disease, phenotype, literature, etc.

Data resources update

Data resources clinvar date:2018/10

Data resources dbvar date:2018/10

Data resources dbsnp date:2018/05

Data source

Variant database comprises variant data from web sources, including NCBI dbSNP, dbVar, ClinVar, etc. CNGBdb acquires variant data from these public databases via FTP. All data obtained from FTP are parsed and integrated according to certain meta-information structure, and displayed on the page in order to provide search and retrieval services for users. Every gene record (e.g. https://db.cngb.org/search/variant/rs1313025510/) includes the original source ID which can be clicked to the NCBI dbSNP, dbVar details page. If source is ClinVar, a variant record in ClinVar may contains more than one variant allele ID, So Variant ID in CNGBdb is actually Variant allele ID in ClinVar. CNGBdb provides a link to ClinVar details page via Variant Set ID in CNGBdb variant details page.

CNGBdb complies with the data usage agreement and related requirements of these source databases. If you have any question about the above methods of data references or think that the data references are not reasonable, please contact CNGBdb@cngb.org.


Reference:

1. NCBI: Coordinators NR. Database resources of the National Center for Biotechnology Information. Nucleic acids research. 2018; 46(D1): D8-D13

2. https://www.ncbi.nlm.nih.gov

3. dbSNP: Smigielski EM, Sirotkin K, Ward M, et al. dbSNP: a database of single nucleotide polymorphisms. Nucleic acids research. 2000;28(1):352-5

4. dbvar: Lappalainen I, Lopez J, Skipper L, et al. DbVar and DGVa: public archives for genomic structural variation. Nucleic Acids Res. 2013;41(Database issue):D936–D941. doi:10.1093/nar/gks1213

5. Clinvar: Landrum MJ, Lee JM, Benson M, et al. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic acids research. 2016;44(D1):D862-8.