25350394c4a287c6fa6cc6922f58f9bd70be2d50 abenetpa Fri Aug 28 11:51:07 2020 -0700 improved description according to new track features refs #24850 diff --git src/hg/makeDb/trackDb/human/clinvar.html src/hg/makeDb/trackDb/human/clinvar.html index cc04865..1785c3e 100644 --- src/hg/makeDb/trackDb/human/clinvar.html +++ src/hg/makeDb/trackDb/human/clinvar.html @@ -1,80 +1,84 @@ <h2>Description</h2> <div class="warn-note" style="border: 2px solid #9e5900; padding: 5px 20px; background-color: #ffe9cc;"> <p><span style="font-weight: bold; color: #c70000;">NOTE:</span><br> 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.</p> </div> <p> -This track shows the genomic positions of variants in the +These tracks show the genomic positions of variants in the <a href="https://www.ncbi.nlm.nih.gov/clinvar/" target="_blank">ClinVar database</a>. 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.</p> +evidence. </p> + +<p> +The <b>ClinVar CNVs track</b> displays copy number variants +(CNVs) equal or larger than 50 bp, and the <b>ClinVar SNVs track</b> displays substitutions and +indels shorter than 50 bp. +Until October 2017, all variants with the ClinVar types +<em>copy number gain/loss</em> and <em>DbVar "nsv" accessions</em> were assigned in the CNV +category. Because the ClinVar type no longer captures this information, any variation equal or +larger than 50 bp is now considered a CNV. +</p> <p> <b>Note:</b> 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 href="https://github.com/macarthur-lab/clinvar" target="_blank">a converter</a> to make ClinVar more comparable to VCF files.</p> <h2>Display Conventions and Configuration</h2> <p> -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 genomic locations of ClinVar variants are labelled with the ClinVar variant descriptions. +<b>Mouseover</b> on items 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. </p> -<p>The track is divided into two subtracks, one for copy number variants (CNVs), which are all -variants longer than 50bp, and a second track for shorter substitutions and indels.</p> - <p> -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 no longer capturing this information, anything longer -than 50bp is now considered a CNV.</p> - -<p> -Entries in the ClinVar CNV track are colored -<b><font color="red">red for loss</font></b> and -<B><font color="blue">blue for gain</font></b>. +Entries in the <b>ClinVar CNV track</b> are colored by <b>type of variant</b>: +<b><font color="da2c37">red for loss</font></b>, +<b><font color="294eae">blue for gain</font></b>, and +<b><font color="840876">purple for insertion</font></b>. +A light to dark color gradient indicates the clinical significance of each variant, with the +lightest shade being benign, or others, to the darkest shade being pathogenic. </p> <p> -Entries in the ClinVar short variants track are shaded by clinical annotation: +Entries in the <b>ClinVar SNVs track</b> are colored by <b>clinical significance</b>: <b><font color="red">red for pathogenic</font></b>, -<B><font color="#888">dark grey for uncertain significance or not provided</font></b> and -<B><font color="#000088">dark blue for variant of uncertain significance</font></b> and -<B><font color="#ADD8E6">light blue for conflicting</font></b> and -<B><font color="green">green for benign</font></b>. +<b><font color="000088">dark blue for variant of uncertain significance</font></b>, +<B><font color="#green">green for benign</font></b>, +<B><font color="#888">dark grey for not provided</font></b>, and +<B><font color="#ADD8E6">light blue for conflicting</font></b>. </p> <p> -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 <a href="https://www.ncbi.nlm.nih.gov/clinvar/docs/review_status/" -target="_blank">ClinVar documentation</a>. -</p> +Items can be filtered according to the size of the variant, variant type, clinical significance, +allele origin, and molecular consequence, using the track <b>Configure</b> options. +Each subtrack has separate display controls, as described +<a href="https://genome.ucsc.edu/goldenPath/help/multiView.html">here</a>. <p>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 <a target=_blank href="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/">README file</a> on our download site. </p> <h2>Data updates</h2> <p>ClinVar publishes a new release on the <a href="https://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=ClinVarNews">first Thursday every month</a>