rs534656527
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PM2_Supporting
This summary comes from the ClinGen Evidence Repository: The variant NM_206933.4:c.14419G>A in USH2A is a missense variant predicted to cause substitution of alanine by threonine at amino acid 4807 (p.Ala4807Thr). The filtering allele frequency (the upper threshold of the 95% CI of 5/30782) of the c.14419G>A variant in USH2A is 0.00006365 for South Asian chromosomes by gnomAD v2.1.1, which is lower than the ClinGen Hearing Loss VCEP threshold (<0.00007) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting). In summary, the clinical significance of this variant is uncertain. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: PM2_Supporting (ClinGen Hearing Loss VCEP specifications version 2; 2/21/2024). LINK:https://erepo.genome.network/evrepo/ui/classification/CA246980/MONDO:0019501/005
Frequency
Consequence
ENST00000307340.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
USH2A | NM_206933.4 | c.14419G>A | p.Ala4807Thr | missense_variant | 66/72 | ENST00000307340.8 | NP_996816.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USH2A | ENST00000307340.8 | c.14419G>A | p.Ala4807Thr | missense_variant | 66/72 | 1 | NM_206933.4 | ENSP00000305941 | P1 | |
USH2A | ENST00000674083.1 | c.14419G>A | p.Ala4807Thr | missense_variant | 66/73 | ENSP00000501296 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251366Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135856
GnomAD4 exome AF: 0.0000554 AC: 81AN: 1461886Hom.: 0 Cov.: 31 AF XY: 0.0000564 AC XY: 41AN XY: 727246
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152284Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74448
ClinVar
Submissions by phenotype
not provided Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Aug 07, 2019 | In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 29343940) - |
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 09, 2022 | This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 4807 of the USH2A protein (p.Ala4807Thr). This variant is present in population databases (rs534656527, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with USH2A-related conditions. ClinVar contains an entry for this variant (Variation ID: 198366). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 28, 2015 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 25, 2015 | The p.Ala4807Thr variant in USH2A has not been previously reported in individual s with hearing loss, but has been identified in 5/66724 European chromosomes and 5/16512 South Asian chromosomes by the Exome Aggregation Consortium (ExAC, http ://exac.broadinstitute.org; dbSNP rs534656527). Computational prediction tools a nd conservation analyses do not provide strong support for or against an impact to the protein. In summary, the clinical significance of the p.Ala4807Thr varian t is uncertain. - |
Usher syndrome Uncertain:1
Uncertain significance, reviewed by expert panel | curation | ClinGen Hearing Loss Variant Curation Expert Panel | Feb 21, 2024 | The variant NM_206933.4:c.14419G>A in USH2A is a missense variant predicted to cause substitution of alanine by threonine at amino acid 4807 (p.Ala4807Thr). The filtering allele frequency (the upper threshold of the 95% CI of 5/30782) of the c.14419G>A variant in USH2A is 0.00006365 for South Asian chromosomes by gnomAD v2.1.1, which is lower than the ClinGen Hearing Loss VCEP threshold (<0.00007) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting). In summary, the clinical significance of this variant is uncertain. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: PM2_Supporting (ClinGen Hearing Loss VCEP specifications version 2; 2/21/2024). - |
Usher syndrome type 2A;C3151138:Retinitis pigmentosa 39 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Feb 14, 2017 | - - |
Usher syndrome type 2A Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at