ClinVar Miner

Submissions for variant NM_004100.5(EYA4):c.866C>T (p.Thr289Met)

gnomAD frequency: 0.00067  dbSNP: rs41286200
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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Biesecker Lab/Clinical Genomics Section, National Institutes of Health RCV000171945 SCV000055157 uncertain significance not provided 2013-06-24 criteria provided, single submitter research
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000150681 SCV000198040 benign not specified 2019-02-14 criteria provided, single submitter clinical testing The p.Thr289Met variant in EYA4 is classified as benign because it has been identified in 0.1% of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). ACMG/AMP Criteria applied: BA1.
Eurofins Ntd Llc (ga) RCV000171945 SCV000334447 uncertain significance not provided 2015-09-02 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000387022 SCV000460377 likely benign Autosomal dominant nonsyndromic hearing loss 10 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Illumina Laboratory Services, Illumina RCV001080380 SCV000460378 uncertain significance Dilated cardiomyopathy 1J 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Invitae RCV001080380 SCV000763589 likely benign Dilated cardiomyopathy 1J 2024-01-31 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000171945 SCV001154886 benign not provided 2023-04-01 criteria provided, single submitter clinical testing EYA4: BS1, BS2
GeneDx RCV000171945 SCV001745465 likely benign not provided 2020-12-22 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 23861362, 28798025)
Ambry Genetics RCV002444614 SCV002682553 likely benign Cardiovascular phenotype 2018-05-31 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
PreventionGenetics, part of Exact Sciences RCV004544352 SCV004777495 likely benign EYA4-related disorder 2022-09-21 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Laboratory of Prof. Karen Avraham, Tel Aviv University RCV000387022 SCV005073746 likely pathogenic Autosomal dominant nonsyndromic hearing loss 10 2024-05-08 criteria provided, single submitter research Likely pathogenic by Deafness Variation Database

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