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Smaller software changes are not announced here. A summary of the three-weekly release changes can be found here. For the full list of our daily code changes head to our GitHub page. Lastly, see our credits page for acknowledgments of the data we host.

Aug. 11, 2026 Deleteriousness Predictions: ClinPred for hg19 and hg38

+We are pleased to announce the release of the ClinPred pathogenicity score track for +hg19 and +hg38. +ClinPred is a machine-learning predictor of pathogenicity for nonsynonymous (missense) +single-nucleotide variants, combining existing pathogenicity scores with population allele +frequency from gnomAD. It 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 a 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 +(A, C, G, T). 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 are also set to 0, since ClinPred only scores +missense variants. Positions with no exome coverage are shown as gaps. +

+ +

Genome Browser screenshot of the ClinPred track

ClinPred pathogenicity scores for all possible single-nucleotide +substitutions (A, C, G, and T) at a genomic locus (chr7, GRCh38/hg38). The four ClinPred +subtracks display predicted pathogenicity scores for each possible alternate allele, where +higher scores indicate a greater likelihood that the variant is disease-causing.

+Note: Zoom in until every base is visible at the top of the display; otherwise, +multiple nucleotides will fall under a single pixel, and no score will be shown on the +mouseover tooltip. +

+We would like to thank the ClinPred authors for making the pre-computed scores publicly +available. This track was developed by Lou Nassar and Max Haeussler with QA by Eliza Alde, +Jairo Navarro, and Barali Kitiyakara. +

Jul. 22, 2026 ENCODE4 cCREs and ENCODE4 Regulation tracks released for human (hg38) and mouse (mm10)

We are excited to announce our major release of the ENCODE4 data collection on the UCSC Genome Browser for both the human (hg38/GRCh38) and mouse (mm10/GRCm38) assemblies. This release consists of two major components: the ENCODE Registry of cCREs (candidate Cis-Regulatory Elements) container, and the new ENCODE4 Regulation container, both described in Moore et al., Nature 2026.