c1ba9dbcaee6d59daac43709a1af950915fe4121
abenetpa
  Wed Sep 30 06:42:54 2020 -0700
added CNV color code link and desc. refs #25207

diff --git src/hg/makeDb/trackDb/human/clinvar.html src/hg/makeDb/trackDb/human/clinvar.html
index a7f3661..8edd0f6 100644
--- src/hg/makeDb/trackDb/human/clinvar.html
+++ src/hg/makeDb/trackDb/human/clinvar.html
@@ -33,36 +33,39 @@
 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>
 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>
-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, to the darkest shade being pathogenic.
+Entries in the <b>ClinVar CNVs track</b> are colored by <b>type of variant</b>, among others,
+<b><font color="red">red for loss</font></b>,
+<b><font color="blue">blue for gain</font></b>,
+<b><font color="purple">purple for inversion</font></b>, and
+<b><font color="orange">orange for insertion</font></b>.
+A light-to-dark color gradient indicates the <b>clinical significance</b> of each variant, with the 
+lightest shade being benign, to the darkest shade being pathogenic. Detailed information on the 
+CNV color code is described 
+<a href="https://genome.ucsc.edu/goldenPath/help/hgCnvColoring.html">here</a>. 
 </p>
 
 <p>
 Entries in the <b>ClinVar SNVs track</b> are colored by <b>clinical significance</b>:
 <b><font color="d20000">red for pathogenic</font></b>,
 <b><font color="000088">dark blue for variant of uncertain significance</font></b>,
 <B><font color="#00d200">green for benign</font></b>,
 <B><font color="#888">dark grey for not provided</font></b>, and
 <B><font color="#8979D4">light blue for conflicting</font></b>.
 </p>
 
 <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