ClinVar Miner

Submissions for variant NM_001042492.3(NF1):c.1063-1G>C

dbSNP: rs1555610955
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Human Genetics, Inc, Center for Human Genetics, Inc RCV000659976 SCV000781891 likely pathogenic Neurofibromatosis, type 1 2016-11-01 criteria provided, single submitter clinical testing
GeneDx RCV001756117 SCV002007117 pathogenic not provided 2022-04-22 criteria provided, single submitter clinical testing Observed in an individual with multiple caf-au-lait macules presenting before age 6 months (Tsipi 2008); Canonical splice site variant predicted to result in an in-frame deletion of exon 10; 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: 30308447)
Genome-Nilou Lab RCV000659976 SCV002561627 likely pathogenic Neurofibromatosis, type 1 2022-03-15 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000659976 SCV003461900 pathogenic Neurofibromatosis, type 1 2022-03-17 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 547580). Disruption of this splice site has been observed in individual(s) with neurofibromatosis type 1 (PMID: 14722917, 30308447). This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 9 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).

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