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. Research data is not easy to interpret, and not
+everything shown is necessarily useful. 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 database. +ClinVar is a free, public archive of reports +of the relationships among human variations and phenotypes, with supporting +evidence.
+ ++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. +
+ ++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 on the start position of variants: 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. The VCF position is also available in this track, +as an additional field, at the end of the list of fields, when you click any variant. +It can be extracted using our table browser, the API +or the bigBedToBed tool (see the Data access section below). +And GnomAD has a converter. +
+ ++Items can be filtered according to the size of the variant, variant type, clinical significance, +allele origin, phenotype, and molecular consequence, using the track Configure options. +Each subtrack has separate display controls, as described +here. +
+ ++Entries in the ClinVar SNVs and ClinVar Interpretations tracks are colored by clinical +significance: +
+Entries in the ClinVar CNVs track are colored by type of variant, among others: +
In the ClinVar SNV track, protein-truncating mutations are shown with +triangles, inspired by the Decipher transcript browser. The variants with the +following molecular consequences are considered protein-truncating: nonsense, +frameshift variant, splice acceptor variant, splice donor variant.
+ ++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 +review status. +Stars (0 to 4) provide a graphical representation of the aggregate review status. +
+ ++The variants in the ClinVar Interpretations track are arrange from top to bottom by the variant +classification of each submission: +
+More information about using and understanding the ClinVar data can be found +here. +
+ ++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 +hg19 README file +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 on the track configuration page. +You can find the previous versions of the track organized by month on our +downloads server in the +archive +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 +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 +
+ ++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. +If you email them (clinvar@ncbi.nlm.nih.gov), feel free to CC us, it is always good to learn more about ClinVar. +
+ ++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 +
+ ++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 +ClinVar. +Cold Spring Harb Mol Case Stud. 2018 Feb;4(1). +PMID: 29437798; PMC: PMC5793773 +
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