ClinVar Miner

Submissions for variant NM_001042492.3(NF1):c.5289A>G (p.Gln1763=)

gnomAD frequency: 0.00002  dbSNP: rs199703296
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000129895 SCV000184712 uncertain significance Hereditary cancer-predisposing syndrome 2014-02-25 criteria provided, single submitter clinical testing The c.5289A>G variant (also known as p.Q1763Q) located in coding exon 38, results from an A to G substitution at nucleotide position 5289 of the NF1 gene. This nucleotide substitution does not change the amino acid at codon 1763. This variant was previously reported in the SNPDatabase as rs199703296. Based on data from the 1000 Genomes Project, the G allele has an overall frequency of approximately 0.05% (1/2184) total alleles studied. The highest observed frequency was 0.52% (1/194) Luhya alleles. This nucleotide position is poorly conserved in available vertebrate species. This alteration is predicted to create new alternate splice donor and acceptor sites by the BDGP and ESEfinder in silico models; however, experimental evidence is not currently available. Since supporting evidence is limited at this time, the clinical significance of c.5289A>G remains unclear.
Invitae RCV000546358 SCV000628651 likely benign Neurofibromatosis, type 1 2023-11-01 criteria provided, single submitter clinical testing
GeneDx RCV001588981 SCV001823072 uncertain significance not provided 2021-10-01 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign in association with neurodevelopmental disorders 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; This variant is associated with the following publications: (PMID: 30287823)
Genome-Nilou Lab RCV000546358 SCV002560531 uncertain significance Neurofibromatosis, type 1 2022-03-15 criteria provided, single submitter clinical testing
Ambry Genetics RCV002336284 SCV002640630 likely benign Hereditary cancer-predisposing syndrome; Cardiovascular phenotype 2020-08-18 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.
Fulgent Genetics, Fulgent Genetics RCV002505106 SCV002815198 uncertain significance Neurofibromatosis, familial spinal; Juvenile myelomonocytic leukemia; Neurofibromatosis, type 1; Neurofibromatosis-Noonan syndrome; Café-au-lait macules with pulmonary stenosis 2021-12-30 criteria provided, single submitter clinical testing

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