Accessing and using data in ClinVar

Disclaimer | Web Access | Data for download | APIs | Release cycle

Disclaimer and data use policy

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. NIH does not independently verify the submitted information. If you have questions about the information contained on this website, please see a health care professional. More information about NCBI's disclaimer policy is available.

If you distribute or copy data from ClinVar, we ask that you provide attribution to ClinVar as a data source in publications and websites.

  • You can cite of one the ClinVar publications (e.g. PMID: 29165669)
  • Websites should display the "Powered by NCBI" logo: Powered by NCBI

Methods to access the data

Web access

The data in ClinVar's web site are updated weekly, on Mondays.  The comprehensive data extractions occur weekly, so that data on the web is in sync with data downloaded as XML.

There are multiple ways to identify information in ClinVar on the web.  Our help document provides detailed instructions about constructing queries and interpreting the detailed display that ClinVar provides from its site. There are other sites, however, that provide links to ClinVar based on common content.  These include:

Resource Basis of the link Where the link appears
Table 1. Some resources linking to ClinVar
dbSNP rs# represented in ClinVar Links to the ClinVar VCV pages in the Summary section and links to the ClinVar RCV pages on the Clinical Significance tab on the RefSNP report
dbVar nsv represented in ClinVar Links to ClinVar RCV pages in the Links to Other Resources section
GTR Genes in which variation has been reported in ClinVar Gene-specific link under Molecular Resources on GTR Test pages
NCBI Gene Human genes in which variation has been reported in ClinVar

ClinVar link under Related Information

See variants in ClinVar in the Variation section

MedGen Conditions or findings reported in ClinVar

Gene-specific link under Molecular Resources

ClinVar link under Related Information

OMIM Allelic variants accessioned in ClinVar Allelic variant section
PubMed Citations provided in a ClinVar submission ClinVar link under Related Information
Variation Viewer Locations on the genome for which data are available in ClinVar ClinVar link in the Allele information display

Data for download

ClinVar provides files in several formats and with different degrees of coverage. Suggestions for selecting the file that may best meet your needs are summarized in this overview.  The categories of files, with their update cycle, are detailed in Table 2.

Format and scope Path Coverage Update cycle
Table 2. Files for download
XML: Complete public data set https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ comprehensive weekly
only the release on the first Thursday of the month is archived
VCF: short variants in ClinVar and dbSNP (see our FAQ) https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf/ partial First Thursday of the month
TSV: summary data about variants or genes https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/ comprehensive First Thursday of the month
TSV: disease names and gene-disease relationships https://ftp.ncbi.nlm.nih.gov/pub/clinvar/ comprehensive daily

Application programming interface (API)

Data from ClinVar can be retrieved programmatically via several application programming interfaces (API). These include:

E-utilities and Entrez Direct

As part of NCBI's Entrez system, ClinVar can be accessed by E-utilities, both via web services and a UNIX command line as Entrez Direct. The subset of functions ClinVar currently supports are esearch, esummary, elink, and efetch.

The general approach is to use esearch to find the list of unique identifiers that return records of interest, and then use either esummary (to retrieve an overview of each of those records) or efetch (to retrieve the complete record), based on the identifiers returned by esearch.  esearch uses the same query language that you use interactively, so you can test your query on the web before automating as esearch.

The default format from eutils is XML, but you can specific JSON output as well.

You may note that the content of the document summary that you retrieve by esummary has more data than are displayed on the web.  For example, you can retrieve location data on both GRCh37 and GRCh38 from assembly_set , database identifiers for disorders from trait_refs, the type of variant from variant_type and the source of any gene-variant relationship from gene/source.  For a discussion of how the data returned from esummary corresponds to objects available by ftp, please use this overview.

Function Examples
Use esearch to find unique identifiers of records of interest

find up to 500 records for the gene FGFR3 (and return results in the default XML format)

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=clinvar&term=FGFR3[gene]&retmax=500

find 500 records for the gene FGFR3, excluding variations that include multiple genes, by using the property "single_gene", and return results in the default XML format

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=clinvar&term=FGFR3[gene]+AND+single_gene[prop]&retmax=500

Use esummary to retrieve the document summary of one of the identifiers retrieved in the previous query https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=clinvar&id=65533
Use esummary, and generate a json output

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=clinvar&id=65533&retmode=json

Use elink to determine which databases in NCBI have information related to a specific ClinVar record

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=clinvar&cmd=acheck&id=9

Use elink to retrieve identifiers in a specific NCBI database related to a specific ClinVar record

PubMed uids
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=clinvar&db=pubmed&id=9
or

MedGen
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=clinvar&db=medgen&id=9

Use efetch to retrieve the XML for one or more variation records (XML that is consistent with the VCV XML) based on their id(s). Note rettype=vcv&is_variationid https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=clinvar&rettype=vcv&is_variationid&id=14206,41472&from_esearch=true
Use efetch to retrieve the XML for the most recent version of a VCV accession. Note rettype=vcv https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=clinvar&rettype=vcv&id=VCV000014206
Use efetch to retrieve the XML for a specified version of a VCV accession. Note rettype=vcv https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=clinvar&rettype=vcv&id=VCV000014206.1
Use efetch to retrieve the XML for the most recent version of an RCV accession. Note rettype=clinvarset https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=clinvar&rettype=clinvarset&id=RCV000000606
Use efetch to retrieve the XML for a specified version of an RCV accession. Note rettype=clinvarset https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=clinvar&rettype=clinvarset&id=RCV000000606.3

Release cycle

ClinVar provides monthly, archived, comprehensive data releases with release notes, the first Thursday of each month.  To be notified of these releases, or any other changes, please follow @NCBI_Clinical on Twitter.

The web site is updated weekly on Mondays. Weekly updates to the data release on the ftp site are provided for users who want to keep data synchronized with the ClinVar website. However, the weekly data releases are not archived; only the monthly releases are archived.

Support Center

Last updated: 2020-03-23T21:19:48Z