ClinVar Miner

Submissions for variant NM_001142800.2(EYS):c.5510G>C (p.Trp1837Ser)

gnomAD frequency: 0.00333  dbSNP: rs199689193
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000176624 SCV000228312 likely benign not specified 2014-11-19 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000504628 SCV000464418 uncertain significance Retinitis pigmentosa 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.
Counsyl RCV000665978 SCV000790202 likely benign Retinitis pigmentosa 25 2017-03-17 criteria provided, single submitter clinical testing
Invitae RCV000963176 SCV001110313 benign not provided 2024-01-31 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000665978 SCV001159163 likely benign Retinitis pigmentosa 25 2020-04-09 criteria provided, single submitter clinical testing
GeneDx RCV000963176 SCV001865806 benign not provided 2015-03-03 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 24265693)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000176624 SCV002555712 likely benign not specified 2022-06-07 criteria provided, single submitter clinical testing Variant summary: EYS c.5510G>C (p.Trp1837Ser) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.004 in 153716 control chromosomes in the gnomAD database, including 6 homozygotes. The observed variant frequency is approximately 1.17 fold of the estimated maximal expected allele frequency for a pathogenic variant in EYS causing Retinitis Pigmentosa phenotype (0.0034), strongly suggesting that the variant is benign. c.5510G>C has been reported in the literature in individuals affected with Retinitis Pigmentosa, however it is often observed in the heterozygous state without a variant reported in the second allele and in several studies the variant was considered to be a polymorphism (example Audo_2010, Eisenberger_2013, Wang_2014, Perez-Carro_2016). These reports do not provide unequivocal conclusions about association of the variant with Retinitis Pigmentosa. Six ClinVar submitters have provided assessments for this variant after 2014. Two classified the variant as benign, three as likely benign, and one as VUS. Based on the evidence outlined above, the variant was classified as likely benign.
CeGaT Center for Human Genetics Tuebingen RCV000963176 SCV003917074 benign not provided 2023-05-01 criteria provided, single submitter clinical testing EYS: BP4, BS1, BS2
NIHR Bioresource Rare Diseases, University of Cambridge RCV000504628 SCV000599155 likely benign Retinitis pigmentosa 2015-01-01 no assertion criteria provided research
Natera, Inc. RCV000504628 SCV001459613 benign Retinitis pigmentosa 2020-01-10 no assertion criteria provided clinical testing

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