ee5cab2ba250102cd4cd57bffead0d0ddcb7b082 gperez2 Wed Sep 2 17:44:01 2026 -0700 Restoring "both" so the sentence correctly refers to both track sets, and rewrapping lines over the 100-character limit, in the gnomAD v4.1.1/MPC news announcement per code review feedback on #38213, refs #38166 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index dbd76d1f2b4..3367bfdef29 100644 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -279,66 +279,77 @@ Harvard Medical School, along with Yarin Gal at the University of Oxford, for making the EVE scores publicly available at evemodel.org, and Mafalda Dias, Jonathan Frazer, Debora S. Marks, Rose Orenbuch, and colleagues at Harvard Medical School, the Centre for Genomic Regulation, and collaborating institutions for developing popEVE and making the scores publicly available at pop.evemodel.org. Lou Nassar and Max Haeussler developed these tracks, with QA by Jairo Navarro, Barali Kitiyakara, and Eliza Alde.

Aug. 26, 2026 gnomAD v4.1.1 and MPC tracks for hg38

We are excited to announce the updated Genome Aggregation Database (gnomAD) v4.1.1 tracks for human assembly hg38/GRCh38, and -new gnomAD Missense Deleteriousness Prediction by Constraint (MPC) tracks, found in the gnomAD superTrack. The tracks are:

+new gnomAD Missense Deleteriousness Prediction by Constraint (MPC) tracks, both found in +the gnomAD superTrack. The +tracks are:

gnomAD v4.1.1 +
gnomAD v4.1.1 (composite track): Shows exome and genome variants. This release revises the LOFTEE END_TRUNC GERP distance threshold from -58.0 to 0.0, reclassifying about 79,920 predicted loss-of-function variants from high-confidence to low-confidence.
gnomAD Constraint Metrics +
gnomAD Constraint Metrics (composite track): The v4.1.1 constraint metrics were recomputed - using a Bayesian framework instead of the previous frequentist approach, expanded the coverage model + using a Bayesian framework instead of the previous frequentist approach, expanded the + coverage model from a depth cutoff to allele number, and now include chrX and chrY. gnomAD's recommended LOEUF threshold changed from <0.35 to <0.45 accordingly. The two v4.1.1 subtracks:
- Transcript LoF v4.1.1: gnomAD Predicted Loss of Function Constraint Metrics By Transcript (LOEUF and pLI)
- Transcript Missense v4.1.1: gnomAD Predicted Missense Constraint Metrics By Transcript (Z-scores)
- Transcript LoF v4.1.1: gnomAD Predicted Loss of Function + Constraint Metrics By Transcript (LOEUF and pLI)
- Transcript Missense v4.1.1: gnomAD Predicted Missense + Constraint Metrics By Transcript (Z-scores)
gnomAD MPC (composite +
gnomAD MPC (composite track): Shows a machine-learning score that predicts which missense variants are likely to be deleterious, computed from the gnomAD v4.1.1 release of 730,947 exomes. The score is shown as four allele-specific tracks (A, C, G, T).
gnomAD MPC overlaps: +
gnomAD MPC overlaps: Covering the small subset of variants (about 250,000, or 0.4% of the ~70 million scored variants) that are scored against more than one transcript.

Genome Browser screenshot of the gnomAD v4.1.1 and MPC tracks

gnomAD v4.1.1 exome and genome variants, the LoF and missense constraint tracks, and the four gnomAD MPC allele tracks plus MPC overlaps, at the KCNH1 locus on hg38.

-For more information about the v4.1.1 update, see the gnomAD +For more information about the v4.1.1 update, see the +gnomAD blog post.

We would like to thank the Genome Aggregation Database Consortium for making these data available, and Kaitlin Samocha for providing the MPC score data. We would also like to thank Christopher Lee, Maximilian Haeussler, and Gerardo Perez for their efforts on this release.

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)