ClinVar Miner

Submissions for variant NM_000070.3(CAPN3):c.2440-1G>A

gnomAD frequency: 0.00002  dbSNP: rs886044052
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000726259 SCV000701322 pathogenic not provided 2017-05-12 criteria provided, single submitter clinical testing
Invitae RCV000595361 SCV000952927 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2A 2023-12-15 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 23 of the CAPN3 gene. While this variant is not anticipated to result in nonsense mediated decay, it likely alters RNA splicing and results in a disrupted protein product. This variant is present in population databases (no rsID available, gnomAD 0.007%). Disruption of this splice site has been observed in individual(s) with clinical features of autosomal recessive limb-girdle muscular dystrophy (PMID: 26886200; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 288971). 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.
Revvity Omics, Revvity RCV000726259 SCV002025055 likely pathogenic not provided 2019-03-18 criteria provided, single submitter clinical testing
Baylor Genetics RCV003475916 SCV004211516 likely pathogenic Muscular dystrophy, limb-girdle, autosomal dominant 4 2023-10-22 criteria provided, single submitter clinical testing
Counsyl RCV000595361 SCV000798808 likely pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2A 2019-07-12 no assertion criteria provided clinical testing

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