ClinVar Miner

Submissions for variant NM_001042492.2(NF1):c.3198-4T>C (rs587782218)

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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 RCV000130902 SCV000185811 likely benign Hereditary cancer-predisposing syndrome 2015-08-29 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Other data supporting benign classification,Co-occurence with a mutation in another gene that clearly explains a proband's phenotype
Center for Human Genetics, Inc RCV000196712 SCV000781975 uncertain significance Neurofibromatosis, type 1 2016-11-01 criteria provided, single submitter clinical testing
GeneDx RCV000589461 SCV000525962 benign not provided 2018-01-23 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Genetic Services Laboratory, University of Chicago RCV000433877 SCV000595973 likely benign not specified 2017-05-02 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589461 SCV000696392 benign not provided 2017-08-16 criteria provided, single submitter clinical testing Variant summary: The NF1 c.3198-4T>C variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a damaging outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 283/181400 control chromosomes in gnomAD, predominantly observed in the African subpopulation at a frequency of 0.014668 (253/17248). This frequency is about 70 times the estimated maximal expected allele frequency of a pathogenic NF1 variant (0.0002084), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign.
Invitae RCV000196712 SCV000252680 benign Neurofibromatosis, type 1 2018-01-04 criteria provided, single submitter clinical testing

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