ClinVar Miner

Submissions for variant NM_001042492.3(NF1):c.3975-4G>A

gnomAD frequency: 0.00001  dbSNP: rs760207624
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000574050 SCV000666708 uncertain significance Hereditary cancer-predisposing syndrome 2016-03-21 criteria provided, single submitter clinical testing The c.3975-4G>A intronic variant results from a G to A substitution 4 nucleotides upstream from coding exon 30 in the NF1 gene. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6503 samples (13006 alleles) with coverage at this position. To date, this alteration has been detected with an allele frequency of approximately 0.001% (greater than 110000alleles tested) in our clinical cohort.This nucleotide position is poorly conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is not predicted to have any significant effect on this splice acceptor site; however, direct evidence is unavailable.Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Labcorp Genetics (formerly Invitae), Labcorp RCV000952140 SCV001098617 likely benign Neurofibromatosis, type 1 2024-12-17 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV000952140 SCV001479098 likely benign Neurofibromatosis, type 1 2020-10-26 criteria provided, single submitter clinical testing
Ambry Genetics RCV002377197 SCV002624568 benign Hereditary cancer-predisposing syndrome; Cardiovascular phenotype 2021-06-24 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, 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.
PreventionGenetics, part of Exact Sciences RCV004553267 SCV004776919 likely benign NF1-related disorder 2020-09-08 no assertion criteria provided 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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