ClinVar Miner

Submissions for variant NM_001042492.3(NF1):c.6921+3A>G

dbSNP: rs1085307885
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000489844 SCV000577589 likely pathogenic not provided 2024-03-15 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge; In-silico analysis is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown; A different variant affecting the same splice site (c.6858+3A>T) has been classified as likely pathogenic at GeneDx in association with neurofibromatosis type 1 and leads to abnormal splicing (PMID: 31766501); This variant is associated with the following publications: (PMID: 31766501, Mostafavi2022[abstract])
Labcorp Genetics (formerly Invitae), Labcorp RCV000528456 SCV000628741 pathogenic Neurofibromatosis, type 1 2024-12-18 criteria provided, single submitter clinical testing This sequence change falls in intron 45 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 individuals with clinical features of neurofibromatosis type 1 (PMID: 23656349; External communication, internal data). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 426988). 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. For these reasons, this variant has been classified as Pathogenic.
St. Jude Molecular Pathology, St. Jude Children's Research Hospital RCV000722026 SCV000853202 likely pathogenic Precursor B-cell acute lymphoblastic leukemia 2016-08-08 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000528456 SCV002560224 likely pathogenic Neurofibromatosis, type 1 2022-03-15 criteria provided, single submitter clinical testing

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