ArticleScientific reports2019
Systematic evaluation of gene variants linked to hearing loss based on allele frequency threshold and filtering allele frequency.
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 11 papers.
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Who cites it
11 citing papers in PubMed, 16 citations in OpenAlex.
- Gene supplementation with precise transgene expression rescues hearing loss in a mouse model with an Mpzl2 East Asian founder variant.Molecular therapy : the journal of the American Society of Gene Therapy · 2026Article
- Biallelic variants of SEMA3F are associated with nonsyndromic hearing loss.Molecules and cells · 2025Article
- Best Disease: Global Mutations Review, Genotype-Phenotype Correlation, and Prevalence Analysis in the Israeli Population.Investigative ophthalmology & visual science · 2024Article
- Bioinformatics characterization of variants of uncertain significance in pediatric sensorineural hearing loss.Frontiers in pediatrics · 2024Article
- Differential genetic diagnoses of adult post-lingual hearing loss according to the audiogram pattern and novel candidate gene evaluation.Human genetics · 2022Article
- Clinical Heterogeneity Associated withBiomedicines · 2022Article
- VPMBench: a test bench for variant prioritization methods.BMC bioinformatics · 2021Article
- Advances in genome editing for genetic hearing loss.Advanced drug delivery reviews · 2021Review
- Problems in variation interpretation guidelines and in their implementation in computational tools.Molecular genetics & genomic medicine · 2020Article
- Worldwide carrier frequency and genetic prevalence of autosomal recessive inherited retinal diseases.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Bayesian modeling to predict malignant hyperthermia susceptibility and pathogenicity ofPharmacogenomics · 2019Article
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As the number of genes identified for linkage to hearing loss has been increasing and more public databases have become available, we aimed to systematically evaluate all variants reported for nonsyndromic hearing loss (NSHL) based on their allele frequencies (AFs) in the general population. Among the 3,549 variants in 97 NSHL genes reported as pathogenic/likely pathogenic in ClinVar and HGMD, 1,618 were found in public databases (gnomAD, ExAC, EVS, and 1000G). To evaluate the pathogenicity of these variants, we employed AF thresholds and NSHL-optimized ACMG guidelines. AF thresholds were determined using a high-resolution variant frequency framework and Hardy-Weinberg equilibrium calculation: 0.6% and 0.1% for recessive and dominant genes, respectively. Filtering AFs of variants linked to NSHL were obtained based on AFs reported in gnomAD and ExAC. We found that 48 variants in 23 genes had filtering AFs above the suggested thresholds and assumed that these variants might be benign based on their filtering AFs. 47 variants, except for one notorious high-frequency GJB2 mutation (c.109G > A; p.Val37Ile), were confirmed to be benign/likely benign by the NSHL-optimized ACMG guidelines. The proposed systematic approach will aid in precise evaluation of NSHL variant pathogenicity in the context of filtering AFs, AF thresholds, and NSHL-specific ACMG guidelines, thus improving NSHL diagnostics.
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