ClinVar Miner

Submissions for variant NM_001042492.3(NF1):c.1393-1G>A

dbSNP: rs1131691131
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000704410 SCV000833359 pathogenic Neurofibromatosis, type 1 2020-02-19 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in NF1 are known to be pathogenic (PMID: 10712197, 23913538). This sequence change affects an acceptor splice site in intron 12 of the NF1 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). Disruption of this splice site has been observed in several individuals with clinical features of neurofibromatosis type 1 (Invitae). ClinVar contains an entry for this variant (Variation ID: 580769). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies.
GeneDx RCV003313137 SCV004012376 pathogenic not provided 2023-07-06 criteria provided, single submitter clinical testing Canonical splice site variant predicted to result in an in-frame loss of the adjacent exon in a gene for which loss of function is a known mechanism of disease; Deletions involving coding exons in this gene are frequently reported as pathogenic, regardless of frame prediction (HGMD); Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge; Also known as IVS10a-1G>A; This variant is associated with the following publications: (PMID: 28481359, 26076063)
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden RCV003313137 SCV004026387 pathogenic not provided 2023-05-16 criteria provided, single submitter clinical testing PVS1, PP4, PM2_SUP

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