ClinVar Miner

Submissions for variant NM_000426.4(LAMA2):c.3736-2A>T

gnomAD frequency: 0.00001  dbSNP: rs372715292
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000654722 SCV000776621 pathogenic LAMA2-related muscular dystrophy 2024-02-20 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 25 of the LAMA2 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 LAMA2 are known to be pathogenic (PMID: 18700894, 32904964). This variant is present in population databases (rs372715292, gnomAD 0.02%). Disruption of this splice site has been observed in individual(s) with clinical features of LAMA2-related conditions (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: 543847). 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.
Counsyl RCV000668700 SCV000793344 likely pathogenic Merosin deficient congenital muscular dystrophy 2017-08-23 criteria provided, single submitter clinical testing
GeneDx RCV001556699 SCV001778328 pathogenic not provided 2022-03-30 criteria provided, single submitter clinical testing Canonical splice site variant predicted to result in an in-frame deletion of a critical region; Deletions involving coding exons in this gene are frequently reported as pathogenic, regardless of frame prediction (HGMD); This variant is associated with the following publications: (PMID: 18700894, 34103343)
Baylor Genetics RCV000668700 SCV005059881 likely pathogenic Merosin deficient congenital muscular dystrophy 2024-03-05 criteria provided, single submitter clinical testing

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