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.

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, these are typically a lot larger, and a second track for short substitutions and indels.

Data access

The raw data can be explored interactively with the Table Browser. 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.cse.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 exact procedure is available on Github.

Credits

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