ClinVar Miner

Submissions for variant NM_000267.3(NF1):c.5694G>A (p.Glu1898=) (rs141077224)

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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 RCV000163376 SCV000213916 likely benign Hereditary cancer-predisposing syndrome 2014-10-09 criteria provided, single submitter clinical testing
GeneDx RCV000611445 SCV000717524 likely benign not specified 2017-11-28 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.
Integrated Genetics/Laboratory Corporation of America RCV000611445 SCV000919880 likely benign not specified 2018-03-23 criteria provided, single submitter clinical testing Variant summary: NF1 c.5694G>A alters a conserved nucleotide resulting in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant was observed with an allele frequency of 0.0001 in 276970 control chromosomes (gnomAD). The observed variant frequency within Latino control individuals in the gnomAD database is comparable to the estimated maximal expected allele frequency for a pathogenic variant in NF1 causing Neurofibromatosis Type 1 phenotype (0.00021), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Latino origin. To our knowledge, no occurrence of c.5694G>A in individuals affected with Neurofibromatosis Type 1 and no experimental evidence demonstrating its impact on protein function have been reported. A ClinVar submission from a clinical diagnostic laboratory (evaluation after 2014) cites the variant as "likely benign." Based on the evidence outlined above, the variant was classified as likely benign.
Invitae RCV000196161 SCV000253218 likely benign Neurofibromatosis, type 1 2017-12-23 criteria provided, single submitter clinical testing
PreventionGenetics RCV000679401 SCV000806299 likely benign not provided 2017-08-15 criteria provided, single submitter clinical testing

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