ClinVar Miner

Submissions for variant NM_001142800.2(EYS):c.5644+5G>A

gnomAD frequency: 0.00001  dbSNP: rs794727412
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 6
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000176626 SCV000228314 uncertain significance not provided 2016-12-29 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000176626 SCV001208483 pathogenic not provided 2024-01-25 criteria provided, single submitter clinical testing This sequence change falls in intron 26 of the EYS gene. It does not directly change the encoded amino acid sequence of the EYS protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs794727412, gnomAD 0.05%). This variant has been observed in individual(s) with retinitis pigmentosa (PMID: 29641573, 31960602, 32218477; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 195939). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV000176626 SCV002032813 pathogenic not provided 2023-12-13 criteria provided, single submitter clinical testing Observed in an individual with retinitis pigmentosa in published literature, although this individual had additional variants in the PDE6B gene that may have also contributed to the phenotype (PMID: 29641573); Intronic variant directly or indirectly altering the +5 splice site in a gene for which loss of function is a known mechanism of disease, and splice predictors support a deleterious effect; This variant is associated with the following publications: (PMID: 31047384, 32037395, 36284460, 29641573, 33576794, 31960602, 32218477, 35816039)
3billion RCV002250587 SCV002521143 uncertain significance Retinitis pigmentosa 25 2022-05-22 criteria provided, single submitter clinical testing The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.004%). In silico tools predict the variant to alter splicing and produce an abnormal transcript (SpliceAI: 0.74). Therefore, this variant is classified as uncertain significanceaccording to the recommendation of ACMG/AMP guideline.
Baylor Genetics RCV002250587 SCV004192933 likely pathogenic Retinitis pigmentosa 25 2024-03-18 criteria provided, single submitter clinical testing
Natera, Inc. RCV001272882 SCV001455302 uncertain significance Retinitis pigmentosa 2020-09-16 no assertion criteria provided clinical testing

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.