ClinVar Miner

Submissions for variant NM_001042492.3(NF1):c.5813-1G>A

dbSNP: rs1057518974
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Centre for Mendelian Genomics, University Medical Centre Ljubljana RCV000415207 SCV000493046 likely pathogenic Cafe-au-lait spot; Axillary freckling; Plexiform neurofibroma 2014-01-29 criteria provided, single submitter clinical testing
Invitae RCV001379465 SCV001577268 likely pathogenic Neurofibromatosis, type 1 2023-08-28 criteria provided, single submitter clinical testing This variant has not been reported in the literature in individuals affected with NF1-related conditions. This sequence change affects an acceptor splice site in intron 38 of the NF1 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). ClinVar contains an entry for this variant (Variation ID: 374204). Studies have shown that disruption of this splice site results in skipping of exon 40 and/or deletion of one nucleotide of exon 40 and introduces a premature termination codon (Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. 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.
GeneDx RCV001591053 SCV001817237 pathogenic not provided 2023-02-27 criteria provided, single submitter clinical testing Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; Has not been previously published as pathogenic or benign to our knowledge; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 27535533)
Genome-Nilou Lab RCV001379465 SCV002560151 pathogenic Neurofibromatosis, type 1 2022-03-15 criteria provided, single submitter clinical testing
Baylor Genetics RCV003470369 SCV004199002 likely pathogenic Juvenile myelomonocytic leukemia 2022-01-18 criteria provided, single submitter clinical testing

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