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 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.
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 clinVarMain.bb and clinVarCnv.bb. 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
can also be used to obtain only features within a given range, e.g.
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/clinvar/clinvarMain.bb -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
ClinVar: public archive of interpretations of clinically relevant variants.
Nucleic Acids Res. 2016 Jan 4;44(D1):D862-8.
PMID: 26582918; PMC: PMC4702865