ClinVar Miner

Submissions for variant NM_018418.5(SPATA7):c.94+2T>C

dbSNP: rs786204787
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000169677 SCV000221214 likely pathogenic Leber congenital amaurosis 3 2013-08-08 criteria provided, single submitter clinical testing The 94+2T>C variant in SPATA7 has not been previously reported. This variant occurs in the invariant region (+/- 1/2) of the splice consensus sequence and is predicted to cause altered splicing leading to an abnormal or absent protein. However, this predictive information, in the absence of functional data, is not enough to conclude pathogenicity but does suggest the variant is likely pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV000169677 SCV005853608 likely pathogenic Leber congenital amaurosis 3 2024-12-30 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 2 of the SPATA7 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in SPATA7 are known to be pathogenic (PMID: 19268277, 22334370, 23847139, 26047050, 26261414). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SPATA7-related conditions. ClinVar contains an entry for this variant (Variation ID: 189245). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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