ClinVar Miner

Submissions for variant NM_001042492.3(NF1):c.5793T>C (p.Ile1931=)

gnomAD frequency: 0.00004  dbSNP: rs779114598
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000167490 SCV000218348 likely benign Hereditary cancer-predisposing syndrome 2014-12-30 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Invitae RCV000228618 SCV000284481 likely benign Neurofibromatosis, type 1 2024-01-31 criteria provided, single submitter clinical testing
GeneDx RCV001697201 SCV000727164 likely benign not provided 2019-08-29 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV000167490 SCV002527630 likely benign Hereditary cancer-predisposing syndrome 2020-11-17 criteria provided, single submitter curation
Genome-Nilou Lab RCV000228618 SCV002560847 likely benign Neurofibromatosis, type 1 2022-03-15 criteria provided, single submitter clinical testing
Medical Genetics, University of Parma RCV000228618 SCV002567810 benign Neurofibromatosis, type 1 2022-08-17 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003226230 SCV003922599 likely benign not specified 2023-03-20 criteria provided, single submitter clinical testing Variant summary: NF1 c.5730T>C alters a conserved nucleotide resulting in a synonymous change. One computational tool predicts the variant may affect splicing. However, this prediction has yet to be confirmed by functional studies. The variant allele was found at a frequency of 2.4e-05 in 251072 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.5730T>C has been reported in the literature in individuals affected with breast cancer. These report(s) do not provide unequivocal conclusions about association of the variant with Neurofibromatosis Type 1. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as likely benign.
PreventionGenetics, part of Exact Sciences RCV004552934 SCV004712810 likely benign NF1-related disorder 2020-09-08 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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