ClinVar Miner

Submissions for variant NM_001042492.3(NF1):c.479+5G>A

dbSNP: rs1567818033
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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 RCV000685086 SCV000812558 pathogenic Neurofibromatosis, type 1 2023-10-16 criteria provided, single submitter clinical testing This sequence change falls in intron 4 of the NF1 gene. It does not directly change the encoded amino acid sequence of the NF1 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with neurofibromatosis, type 1 (PMID: 23758643, 27322474). ClinVar contains an entry for this variant (Variation ID: 565507). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 4 and introduces a premature termination codon (PMID: 23758643, 27322474). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV002509509 SCV002818972 pathogenic not provided 2023-01-04 criteria provided, single submitter clinical testing Non-canonical splice site variant demonstrated to cause aberrant splicing and predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease (Evans et al., 2016); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 23906300, 23758643, 27322474, 35885913)
Baylor Genetics RCV003465553 SCV004190739 pathogenic Juvenile myelomonocytic leukemia 2023-05-06 criteria provided, single submitter clinical testing

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