ClinVar Variants Track Settings
ClinVar Variants   (All Phenotype and Literature tracks)

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 ClinVar Nucl.  ClinVar Nucleotide Variants   schema 
 ClinVar CNVs  ClinVar Copy-Number Variants   schema 


ClinVar is intended for use primarily by physicians and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine. While the ClinVar database is open to all academic users, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal questions.

This track shows the genomic positions of variants in the ClinVar database. ClinVar is a free, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. The track is updated after every ClinVar release, once a month.

Note: The data in the track are obtained directly from ClinVar's FTP site. We display the data obtained from ClinVar as-is to avoid discrepancies between UCSC and NCBI. However, be aware that the ClinVar conventions are different from the VCF standard. Variants may be right-aligned or may contain additional context, e.g. for inserts. ExAC/gnomAD make available a converter to make ClinVar more comparable to VCF files.

Display Conventions and Configuration

Genomic locations of ClinVar variants are labeled with the ClinVar variant descriptions. All information related to each is variant is shown on that variant's details page. Leave the mouse over a feature for more than 2 seconds to show the clinical significance of a variant.

The track is divided into two subtracks, one for copy number variants (CNVs), which are typically larger, and a second track for short substitutions and indels.

Entries in the ClinVar CNVs track are colored red for loss and blue for gain.

Data access

The raw data can be explored interactively with the Table Browser or the Data Integrator.

For automated download and analysis, the genome annotation is stored in a bigBed file that can be downloaded from our download server. The files for this track are called and Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, e.g. bigBedToBed -chrom=chr21 -start=0 -end=100000000 stdout

You can find previous versions of the ClinVar tracks organized by month on our download server here.


ClinVar files were reformatted at UCSC to the bigBed format. The data is updated every month, one week after the ClinVar release date. The program that performs the update is available on Github.


Thanks to NCBI for making the ClinVar data available on their FTP site as a tab-separated file.


Landrum MJ, Lee JM, Benson M, Brown G, Chao C, Chitipiralla S, Gu B, Hart J, Hoffman D, Hoover J et al. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res. 2016 Jan 4;44(D1):D862-8. PMID: 26582918; PMC: PMC4702865