ClinVar Miner

Submissions for variant NM_001042492.3(NF1):c.2002-1G>A

dbSNP: rs1555613743
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 4
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000578644 SCV000680719 pathogenic not provided 2017-12-27 criteria provided, single submitter clinical testing The c.2002-1G>A splice site variant in the NF1 gene has been previously reported in at least one individual with a clinical diagnosis of neurofibromatosis type 1 (Griffiths et al., 2007). This pathogenic variant destroys the canonical splice acceptor site in intron 17, and is expected to cause abnormal gene splicing. The c.2002-1G>A variant is not observed in large population cohorts (Lek et al., 2016). Based on currently available evidence, we consider c.2002-1G>A to be pathogenic.
Center for Human Genetics, Inc, Center for Human Genetics, Inc RCV000660002 SCV000781934 pathogenic Neurofibromatosis, type 1 2016-11-01 criteria provided, single submitter clinical testing
Invitae RCV000660002 SCV000827499 pathogenic Neurofibromatosis, type 1 2023-11-01 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 17 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 NF1-related conditions (PMID: 16944272, 31370276). ClinVar contains an entry for this variant (Variation ID: 488815). 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 RCV000660002 SCV002561724 pathogenic Neurofibromatosis, type 1 2022-03-15 criteria provided, single submitter clinical testing

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.