ClinVar Miner

Submissions for variant NM_025136.4(OPA3):c.143-5C>A

gnomAD frequency: 0.00003  dbSNP: rs770452409
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000521565 SCV000619223 uncertain significance not provided 2018-08-20 criteria provided, single submitter clinical testing The c.143-5 C>A variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.143-5 C>A variant is observed in 4/30,048 (0.01%) alleles from individuals of South Asian background in the ExAC dataset (Lek et al., 2016). Several in silico splice prediction models predict that creates a cryptic acceptor site which may supplant the natural acceptor site and lead to abnormal gene splicing. However, in the absence of RNA/functional studies, the actual effect of this sequence change in this individual is unknown. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Labcorp Genetics (formerly Invitae), Labcorp RCV003766954 SCV004581523 uncertain significance 3-Methylglutaconic aciduria type 3; Optic atrophy 3 2023-08-11 criteria provided, single submitter clinical testing This sequence change falls in intron 1 of the OPA3 gene. It does not directly change the encoded amino acid sequence of the OPA3 protein. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with OPA3-related conditions. ClinVar contains an entry for this variant (Variation ID: 450618). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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.
Natera, Inc. RCV001829494 SCV002088921 uncertain significance 3-Methylglutaconic aciduria type 3 2019-11-11 no assertion criteria provided clinical testing

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