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

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Show only items with ClinVar Star-Rating (0-4) at or above:   (range: 0 to 1000)

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 ClinVar Short Variants  ClinVar Short Variants <= 100bp   schema 
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 ClinVar Long Variants  ClinVar Long Variants > 100bp (mostly Copy-Number Variants)   schema 

Description

NOTE:
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 all variants longer than 100bp, and a second track for shorter substitutions and indels.

Until October 2017, all variants with the ClinVar types copy number gain/loss and DbVar "nsv" accessions were put in the CNV category. Due to the ClinVar type not capturing this information anymore, anything longer than 100bp is now considered a CNV.

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

Entries in the ClinVar short variants track are shaded by clinical annotation: red for pathogenic, dark grey for uncertain significance or not provided and green for benign.

The score of the variants is the number of "stars" in ClinVar. On the track configuration page (above), you can filter the track to show only variants with more than a certain number of stars. For more information on the star rating, see the ClinVar documentation.

On the human assembly hg19, no variants on the mitochondrial genome are shown, as the mitochondrial genome was not part of the human genome when it was released. The version of "chrM" that was selected from Genbank by UCSC when the hg19 assembly was packaged is different than the version added by NCBI when they added an "MT" sequence later. Since the mitochondrial sequence differs, the variant positions cannot be converted reliably.

Data updates

ClinVar publishes a new release on the first Thursday every month and this track is 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 archive directory. To access one of these previous versions, paste the URL to one of the older files into our "Custom tracks" box.

Data access

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 here. The tool 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

Methods

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.

Credits

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

References

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