bafa5b1fa3546c23f9091e08304355490ded9ead lrnassar Tue May 26 11:34:39 2026 -0700 Address CR feedback on v498 description pages. refs #37533 varFreqs.html: fix contact-us sentence punctuation/grammar, replace "ships" with "provides"/"includes" in two spots, and rewrite the "trackUI labels" sentence to refer to the track configuration page and the combined-track bigBed (per Gerardo's question about what trackUI labels meant). clinPred.html: replace em-dashes around "those that do not change the encoded amino acid" with commas. predictionScoresSuper.html: reorder references alphabetically by first author. diff --git src/hg/makeDb/trackDb/human/clinPred.html src/hg/makeDb/trackDb/human/clinPred.html index 1748d7654b5..c24f8529d37 100644 --- src/hg/makeDb/trackDb/human/clinPred.html +++ src/hg/makeDb/trackDb/human/clinPred.html @@ -1,126 +1,126 @@ <h2>Description</h2> <p> This track collection shows <a href="https://sites.google.com/site/clinpred/" target="_blank">ClinPred</a> scores, a machine-learning predictor of pathogenicity for nonsynonymous (missense) single-nucleotide variants. ClinPred combines existing pathogenicity scores with population allele frequency from gnomAD, and was trained on confidently annotated disease-causing and benign variants from ClinVar. Pre-computed scores are provided for all possible human missense variants in the exome. </p> <p> Scores range from 0 to 1, with higher values indicating greater predicted likelihood that a variant is disease-relevant. The authors recommend a score of ≥ 0.5 as evidence of pathogenicity. As with any pathogenicity prediction score, ClinPred is intended as supporting evidence rather than a stand-alone classifier. </p> <h2>Display Conventions and Configuration</h2> <p> There are four subtracks in this collection, one for each possible alternate nucleotide. At every exome position covered by ClinPred, three of the four subtracks show a score (one per non-reference base) and the fourth, corresponding -to the reference base, is set to 0. Synonymous alternates — those that do -not change the encoded amino acid — are also set to 0, since ClinPred only +to the reference base, is set to 0. Synonymous alternates, those that do +not change the encoded amino acid, are also set to 0, since ClinPred only scores missense variants. Positions with no exome coverage are shown as gaps. </p> <p> When using this track, zoom in until you can see every basepair at the top of the display. Otherwise, several nucleotides fall under each pixel and no score will be shown on the mouseover tooltip. </p> <p><b>Track colors</b></p> <p> Each subtrack is colored by score using the threshold recommended by the ClinPred authors: </p> <table style="text-align: left;"> <thead> <tr> <th>Range</th> <th>Classification</th> </tr> </thead> <tbody> <tr> <td>≥ 0.5</td> <td style="color: rgb(255,0,0);">Likely pathogenic</td> </tr> <tr> <td>< 0.5</td> <td style="color: rgb(80,166,230);">Likely benign</td> </tr> </tbody> </table> <h2>Data Access</h2> <p> ClinPred scores are available at the <a href="https://sites.google.com/site/clinpred/" target="_blank">ClinPred website</a>, which provides pre-computed scores for all possible human missense variants. </p> <p> The ClinPred data on the UCSC Genome Browser can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. For automated download and analysis, the data are stored in bigWig files and can be downloaded from <a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/clinPred/" target="_blank">our download server</a>. The files are named <tt>a.bw, c.bw, g.bw, t.bw</tt>. Individual regions can be obtained using <tt>bigWigToBedGraph</tt>, which can be compiled from source or downloaded as a precompiled binary; instructions are <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">here</a>. For example: <br> <br> <tt>bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/$db/clinPred/a.bw stdout</tt> </p> <h2>Methods</h2> <p> Data were downloaded from the <a href="https://sites.google.com/site/clinpred/" target="_blank">ClinPred website</a> on May 5, 2026, and converted into four per-alternate-base bigWig files using a custom script. As with all other tracks, a full log of the commands used for the conversion is available in our <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/" target="_blank">source repository</a>, for <a href="https://raw.githubusercontent.com/ucscGenomeBrowser/kent/master/src/hg/makeDb/doc/hg19.txt" target="_blank">hg19</a> and <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/clinPred.txt" target="_blank">hg38</a>. </p> <h2>Data Use</h2> <p> ClinPred scores are freely available for non-commercial applications. For commercial use, please see the licensing information on the <a href="https://sites.google.com/site/clinpred/" target="_blank">ClinPred website</a>. </p> <h2>Credits</h2> <p> Thanks to the ClinPred authors for making the pre-computed scores available through their website. </p> <h2>References</h2> <p> Alirezaie N, Kernohan KD, Hartley T, Majewski J, Hocking TD. <a href="https://linkinghub.elsevier.com/retrieve/pii/S0002-9297(18)30271-4" target="_blank"> ClinPred: Prediction Tool to Identify Disease-Relevant Nonsynonymous Single-Nucleotide Variants</a>. <em>Am J Hum Genet</em>. 2018 Oct 4;103(4):474-483. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30220433" target="_blank">30220433</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6174354/" target="_blank">PMC6174354</a> </p>