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.
These tracks show 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
The ClinVar SNVs track displays substitutions and indels shorter than 50 bp and
the ClinVar CNVs track displays copy number variants (CNVs) equal or larger than 50 bp.
Until October 2017, all variants with the ClinVar types
copy number gain/loss and DbVar "nsv" accessions were assigned in the CNV
category. Because the ClinVar type no longer captures this information, any variation equal to or
larger than 50 bp is now considered a CNV.
The ClinVar Interpretations track displays the genomic positions of individual variant
submissions and interpretations of the clinical significance and their relationship to disease in
the ClinVar database.
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
Items can be filtered according to the size of the variant, variant type, clinical significance,
allele origin, and molecular consequence, using the track Configure options.
Each subtrack has separate display controls, as described
Mouseover on the genomic locations of ClinVar variants shows variant details, clinical
interpretation, and associated conditions. Further information on each variant is displayed on
the details page by a click onto any variant. ClinVar is an archive for assertions of clinical
significance made by the submitters. The level of review supporting the assertion of clinical
significance for the variation is reported as the
Stars (0 to 4) provide a graphical representation of the aggregate review status.
Entries in the ClinVar CNVs track are colored by type of variant, among others:
A light-to-dark color gradient indicates the clinical significance of each variant, with the
lightest shade being benign, to the darkest shade being pathogenic. Detailed information on the
CNV color code is described
- red for loss
- blue for gain
- purple for inversion
- orange for insertion
Entries in the ClinVar SNVs and ClinVar Interpretations tracks are colored by clinical
- red for pathogenic
- dark blue for variant of uncertain significance
- green for benign
- dark grey for not provided
- light blue for conflicting
The variants in the ClinVar Interpretations track are sorted by the variant
classification of each submission:
The size of the bead represents
the number of submissions at that genomic position. For track display clarity, these submission
numbers are binned into three categories:
- P: Pathogenic
- LP: Likely Pathogenic
- VUS: Variant of Unknown Significance
- LB: Likely Benign
- B: Benign
- OTH: Others
Hovering on the track items shows the genomic variations which start at that position
and the number of individual submissions with that classification. The details page lists all
rated submissions from ClinVar, with specific details to the interpretation of the clinical or
functional significance of each variant in relation to a condition. Interpretation is at
variant-level, not at case (or patient-specific) level.
- Small-sized beads: 1-2 submissions
- Medium-sized beads: 3-7 submissions
- Large-sized beads: 8 or more submissions
More information about using and understanding the ClinVar data can be found
For the human genome version hg19: the hg19 genome released by UCSC in 2009 had a
mitochondrial genome "chrM" that was not the same as the one later used for most
databases like ClinVar. As a result, we added the official mitochondrial genome
in 2020 as "chrMT" and all mitochondrial annotations of ClinVar and most other
databases are shown on the mitochondrial genome called "chrMT". For full description
of the issue of the mitochondrial genome in hg19, please see the
on our download site.
ClinVar publishes a new release on the
first Thursday every month.
This track is then updated automatically at most six days
later. The exact date of our last update is shown when you click onto any variant.
You can find the previous versions of the track organized by month on our
downloads server in the
directory. To display one of these previous versions, paste the URL to one of
the older files into the custom track text input field under "My Data > Custom Tracks".
The raw data can be explored interactively with the Table Browser
or the Data Integrator. The data can be
accessed from scripts through our API, the track names are
"clinVarMain and "clinVarCnv".
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
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
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.
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Azzariti DR, Riggs ER, Niehaus A, Rodriguez LL, Ramos EM, Kattman B, Landrum MJ, Martin CL, Rehm HL.
Points to consider for sharing variant-level information from clinical genetic testing with
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