ClinVar Miner

Submissions for variant NM_001042492.3(NF1):c.2850+1G>A

dbSNP: rs1131691122
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Total submissions: 5
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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 RCV000660021 SCV000781963 pathogenic Neurofibromatosis, type 1 2016-11-01 criteria provided, single submitter clinical testing
Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital RCV000660021 SCV000897649 pathogenic Neurofibromatosis, type 1 2019-04-02 criteria provided, single submitter clinical testing
3billion RCV001775145 SCV002011926 pathogenic Neurofibromatosis-Noonan syndrome 2021-10-02 criteria provided, single submitter clinical testing Canonical splice site: predicted to alter splicing and result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant (PVS1_VS). It is not observed in the gnomAD v2.1.1 dataset (PM2). The variant has been reported multiple times as an established pathogenic variant (ClinVar ID: VCV000547617.2). Patient's phenotype is considered compatible with Neurofibromatosis-Noonan syndrome (3billion dataset, PP4). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline
Invitae RCV000660021 SCV002117451 pathogenic Neurofibromatosis, type 1 2022-05-08 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 21 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: 16944272, 18546366, 27999334, 31370276). ClinVar contains an entry for this variant (Variation ID: 547617). 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.
Genome-Nilou Lab RCV000660021 SCV002561807 pathogenic Neurofibromatosis, type 1 2022-03-15 criteria provided, single submitter clinical testing

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