ArticleScientific reports2019
REVEL and BayesDel outperform other in silico meta-predictors for clinical variant classification.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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Who cites it
73 citing papers in PubMed.
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- Identification and functional validation of a novel disease-causing variant in the noncoding region of NYX.Acta ophthalmologica · 2026Article
- An integrated, scaled approach to resolve TSC2 variants of uncertain significance.Nature communications · 2026Article
- Fanconi Anemia as a Window into Premalignant Field Cancerization of the Oral Mucosa.medRxiv : the preprint server for health sciences · 2026Article
- Genomic landscape of drug binding and pharmacogenetic variation across diverse populations using SNPdrug3D.Nature communications · 2026Article
- Artificial Intelligence in Rare Diseases: Workflow-Integrated Precision Kidney Care.Clinics and practice · 2026Review
- Tutorial for variant interrogation in tumor samples.PLoS computational biology · 2026Article
- Introducing iCatalog as a clinical decision support tool for collaborative pediatric precision oncology studies.Communications medicine · 2026Article
- Comprehensive analysis of non-synonymous single-nucleotide polymorphism of human TSC1 and TSC2 genes: An in silico approach.PloS one · 2026Article
- Recognition of a Critical Functional Domain and ImprovedHuman mutation · 2026Article
- Reclassification of missense variant pathogenicity using ClinGen recommendations for recalibrated PP3/BP4 in silico predictor score thresholds.Genetics in medicine open · 2026Article
- Non-recurrent duplications on chromosome 4p16.1 involving cis-regulatory elements affecting neural crest development in patients with isolated bilateral microtia.Human genetics · 2025Article
- Calibrated Variant Effect Prediction at the Residue Level Using Conditional Score Distributions.bioRxiv : the preprint server for biology · 2025Article
- Prevalence of MUTYH Monoallelic Variants in Patients With Hereditary Cancer Using Multigene Panel Testing.Cancer medicine · 2025Article
- Making Sense of Missense: Benchmarking MutScore for Variant Interpretation in Inherited Cardiac Diseases.Molecular diagnosis & therapy · 2025Article
- NKX2-5 congenital heart disease mutations show diverse loss and gain of epigenomic, biochemical and chromatin search functions underpinning pathogenicity.bioRxiv : the preprint server for biology · 2025Article
- Expanding the Genomic Landscape of HBOC and Cancer Risk Among Mutation Carriers.International journal of molecular sciences · 2025Article
- A Report of a Child with SEC31A-Related Neurodevelopmental Disorder.International journal of molecular sciences · 2025Article
- A series of reviews in familial cancer: genetic cancer risk in context variants of uncertain significance in MMR genes: which procedures should be followed?Familial cancer · 2025Review
13 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many in silico predictors of genetic variant pathogenicity have been previously developed, but there is currently no standard application of these algorithms for variant assessment. Using 4,094 ClinVar-curated missense variants in clinically actionable genes, we evaluated the accuracy and yield of benign and deleterious evidence in 5 in silico meta-predictors, as well as agreement of SIFT and PolyPhen2, and report the derived thresholds for the best performing predictor(s). REVEL and BayesDel outperformed all other meta-predictors (CADD, MetaSVM, Eigen), with higher positive predictive value, comparable negative predictive value, higher yield, and greater overall prediction performance. Agreement of SIFT and PolyPhen2 resulted in slightly higher yield but lower overall prediction performance than REVEL or BayesDel. Our results support the use of gene-level rather than generalized thresholds, when gene-level thresholds can be estimated. Our results also support the use of 2-sided thresholds, which allow for uncertainty, rather than a single, binary cut-point for assigning benign and deleterious evidence. The gene-level 2-sided thresholds we derived for REVEL or BayesDel can be used to assess in silico evidence for missense variants in accordance with current classification guidelines.
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Registered trials
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