Jin Yu

We are excited to announce the release of dbNSFP v5.3, featuring an expansion of 1.6 million new possible nsSNVs (non-synonymous SNVs) and ssSNVs (splice site SNVs) derived from newly added protein-coding transcripts in GENCODE Human Release 49 using long read NGS data.
www.dbnsfp.org/releases

v5.3 release also include MisFit scores v1.5.1, a novel method to estimate missense fitness effects using a graphical model (thanks to Dr. Yufeng Shen from Columbia University, doi: 10.1038/s41467-025-59937-2).

dbNSFP - Highlights in dbNSFP v5.1 Highlights in dbNSFP v5.1 March 21, 2025 Jin Yu & Xiaoming Liu

📋 Also check dbNSFP v5.1, which included allele frequency data from 1.5 million general healthy individuals to improve rare variant interpretation:
www.dbnsfp.org/blog/highlig...

dbNSFP - Releases Current Release: dbNSFP v5.2 (July 2, 2025) (README v5.2a, README v5.2c, Change Log) Rebuilt variant set for all possible nsSNVs and ssSNVs based on latest GENCODE release 48 (Ensembl v114). Added ...

These updates provide more comprehensive and accurate variant interpretation capabilities, particularly valuable for clinical genomics applications and VUS classification.

📋 Check the detailed release notes: www.dbnsfp.org/releases

dbNSFP - Releases Current Release: dbNSFP v5.2 (July 2, 2025) (README v5.2a, README v5.2c, Change Log) Rebuilt variant set for all possible nsSNVs and ssSNVs based on latest GENCODE release 48 (Ensembl v114). Added ...

Key Updates in v5.2:
- Rebuilt variant set for all possible nsSNVs and ssSNVs based on the latest GENCODE release 48
- Added MutPred2 (thanks to Drs. Timothy Bergquist and Vikas Pejaver)
- Updated ESM1b scores (thanks to Drs. Po-Yu Lin and Nadav Brandes)
- Added GenCC for gene-disease associations

dbNSFP - Releases Current Release: dbNSFP v5.2 (July 2, 2025) (README v5.2a, README v5.2c, Change Log) Rebuilt variant set for all possible nsSNVs and ssSNVs based on latest GENCODE release 48 (Ensembl v114). Added ...

We are pleased to announce the release of dbNSFP v5.2, featuring several major updates that will enhance variant annotation and pathogenicity prediction workflows.

用这种方式混淆是非的人可能就是孔子所说的: 鄉愿，德之贼也。

Special thanks to Drs. Jacek Majewski, Weiva Sieh, and Ogün Adebali for updating the licenses to allow their scores to be included in the dbNSFP commercial version.

The updated score licenses are detailed in the dbNSFP README file.

dbNSFP - Releases Current Release: dbNSFP v5.1 (March 21, 2025) (Highlights, README v5.1a, Change Log) Rebuilt variant set (all potential nsSNVs and ssSNVs) based on latest GENCODE release 47 (Ensembl v113). Added Al...

We’ve just released a minor update to the dbNSFP commercial branch v5.1.1c, which now includes ClinPred, REVEL, and PHACTboost scores.

www.dbnsfp.org/releases

As a philosopher of science, Karl Popper was not attempting to guide scientific research using philosophy (as many others did), conversely, he learned the spirit of science and used it to critique conventional philosophers and religions rooted in the pre-scientific era.

Nice sum up for the spirit of science. Ironically, I was never taught this during my time as a physics student at Fudan. Instead, I first encountered Karl Popper's concept of falsification when I read his famous book: "The Open Society and Its Enemies" right after graduation.

Thanks! Erik.

Jin Yu ‪Co-founder at Genos Bioinformatics LLC‬ - ‪‪Cited by 39,260‬‬ - ‪Next Generation Sequencing‬ - ‪Bioinformatics‬ - ‪Genomics‬ - ‪Statistical Genetics‬

scholar.google.com/citations?us...

dbNSFP - Download Download dbNSFP for Academic and Non-commercial Use dbNSFP is free for academic and non-commercial use under the CC4-NC-NDR license. Please complete the academic user registration to receive the downl...

All these scores are readily available in dbNSFP: www.dbnsfp.org/download

Among the 60 missense variant effect predictors evaluated, MetaRNN (from dbNSFP team) and ClinPred were the top Meta-predictors on the full evaluation data set (Fig. 1) with AUROC=0.92, while AlphaMissense was the top individual predictor with AUROC=0.88.

Critical assessment of missense variant effect predictors on disease-relevant variant data - Human Genetics Regular, systematic, and independent assessments of computational tools that are used to predict the pathogenicity of missense variants are necessary to evaluate their clinical and research utility an...

We are pleased to share the latest CAGI (Critical Assessment of Genome Interpretation) report on the Annotate-All-Missense (Missense Marathon) challenge has been peer-reviewed and published.

link.springer.com/article/10.1...

Can you please add me to the science feed? Thanks.

google school profile scholar.google.com/citations?us...

4. Additionally, the dbNSFP team evaluated how the accumulated gene definitions improvement made in GENCODE (specifically from V46 to V47) impacts variant annotations in dbNSFP (from v5.0 to v5.1).

3. We believe this resource will not only help clinical genomic variant interpretations, but also help basic research for complex diseases such as schizophrenia and coronary artery disease, using the ultra-rare variants strategies with this much expanded reference population.

2. Some of the datasets are first-time distributed to the general public (e.g., All of Us 250K genomes) thanks to collaboration with @moezdawood.bsky.social and Dr. Richard Gibbs from HGSC at Baylor College of Medicine.

dbNSFP - Highlights in dbNSFP v5.1 Highlights in dbNSFP v5.1 March 21, 2025 Jin Yu & Xiaoming Liu

1. dbNSFP just made a new release v5.1, which now includes variant allele frequencies among ~1.5 million individuals aggregated from largest sequencing projects such as gnomAD (including UKB WES), TOPMed, All of Us and Regeneron 1M WES.

www.dbnsfp.org/blog/highlig...