ClinVar Miner

Submissions for variant NM_001042492.3(NF1):c.7970+5G>T

dbSNP: rs1567627286
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000680833 SCV000808281 likely pathogenic not provided 2024-10-22 criteria provided, single submitter clinical testing Intronic variant directly or indirectly altering the +5 splice site in a gene for which loss of function is a known mechanism of disease, and splice predictors support a deleterious effect; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 15146469, 25074460)
Labcorp Genetics (formerly Invitae), Labcorp RCV001377738 SCV001575147 likely pathogenic Neurofibromatosis, type 1 2023-12-25 criteria provided, single submitter clinical testing This sequence change falls in intron 53 of the NF1 gene. It does not directly change the encoded amino acid sequence of the NF1 protein. It affects a nucleotide within the consensus splice site. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with clinical features of NF1-related conditions (PMID: 25074460). ClinVar contains an entry for this variant (Variation ID: 561510). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant disrupts the c.7907+5G nucleotide in the NF1 gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 15146469, 25074460). This suggests that this nucleotide is clinically significant, and that variants that disrupt this position are likely to be disease-causing. 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.
Genome-Nilou Lab RCV001377738 SCV002560599 likely pathogenic Neurofibromatosis, type 1 2022-03-15 criteria provided, single submitter clinical testing

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