+This track collection shows +ClinPred +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. +
+ ++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. +
+ ++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 +scores missense variants. Positions with no exome coverage are shown as gaps. +
+ ++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. +
+ +Track colors
+ ++Each subtrack is colored by score using the threshold recommended by the +ClinPred authors: +
+ +| Range | +Classification | +
|---|---|
| ≥ 0.5 | +Likely pathogenic | +
| < 0.5 | +Likely benign | +
+ClinPred scores are available at the +ClinPred +website, which provides pre-computed scores for all possible human missense +variants. +
+ +
+The ClinPred data on the UCSC Genome Browser can be explored interactively with
+the Table Browser or the
+Data Integrator. For automated download
+and analysis, the data are stored in bigWig files and can be downloaded from
+our
+download server. The files are named a.bw, c.bw, g.bw, t.bw.
+Individual regions can be obtained using bigWigToBedGraph, which can
+be compiled from source or downloaded as a precompiled binary; instructions
+are here.
+For example:
+
+bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/$db/clinPred/a.bw stdout
+
+Data were downloaded from the +ClinPred +website 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 +source repository, for +hg19 and +hg38. +
+ ++ClinPred scores are freely available for non-commercial applications. For +commercial use, please see the licensing information on the +ClinPred +website. +
+ ++Thanks to the ClinPred authors for making the pre-computed scores available +through their website. +
+ ++Alirezaie N, Kernohan KD, Hartley T, Majewski J, Hocking TD. + +ClinPred: Prediction Tool to Identify Disease-Relevant Nonsynonymous Single-Nucleotide Variants. +Am J Hum Genet. 2018 Oct 4;103(4):474-483. +PMID: 30220433; PMC: PMC6174354 +