ClinVar Miner

Submissions for variant NM_001042492.3(NF1):c.654+2T>C

dbSNP: rs2143774762
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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 RCV001353319 SCV001584209 pathogenic Neurofibromatosis, type 1 2025-01-06 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 6 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 (NF1) and/or NF1-Noonan syndrome (PMID: 21354044; internal data). ClinVar contains an entry for this variant (Variation ID: 1048732). 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 RCV005051897 SCV005685809 pathogenic not provided 2024-07-26 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; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 31776437)
Laboratory of Medical Genetics, National & Kapodistrian University of Athens RCV001353319 SCV001548450 pathogenic Neurofibromatosis, type 1 2019-01-01 no assertion criteria provided clinical testing

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