ClinVar Miner

Submissions for variant NM_001042492.3(NF1):c.1641+1G>A

dbSNP: rs1555612866
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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 RCV000529214 SCV000628378 pathogenic Neurofibromatosis, type 1 2024-01-29 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 14 of the NF1 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 NF1 are known to be pathogenic (PMID: 10712197, 23913538). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with clinical features of neurofibromatosis type 1 (PMID: 10712197, 30308447; Invitae). ClinVar contains an entry for this variant (Variation ID: 457539). 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.
GeneDx RCV000786797 SCV001778136 likely pathogenic not provided 2024-02-14 criteria provided, single submitter clinical testing Observed in a pediatric patient with multiple cafe-au-lait macules (PMID: 30308447); 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 of this gene are a known mechanism of disease (HGMD); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 28422736, 22155606, 14635100, 30308447, 25486365)
Genome-Nilou Lab RCV000529214 SCV002561683 likely pathogenic Neurofibromatosis, type 1 2022-03-15 criteria provided, single submitter clinical testing
MutSpliceDB: a database of splice sites variants effects on splicing, NIH RCV000786797 SCV000925687 not provided not provided no assertion provided in vitro

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