ClinVar Miner

Submissions for variant NM_000267.3(NF1):c.4206A>G (p.Glu1402=) (rs17886566)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163442 SCV000213989 likely benign Hereditary cancer-predisposing syndrome 2014-08-05 criteria provided, single submitter clinical testing
GeneDx RCV000679390 SCV000526582 likely benign not provided 2018-04-10 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 RCV000249721 SCV000917882 benign not specified 2018-01-02 criteria provided, single submitter clinical testing Variant summary: The NF1 c.4206A>G (p.Glu1402Glu) variant involves the alteration of a conserved nucleotide located in the Ras GTPase-activating protein domain (InterPro), resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 4/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 212/277040 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.008197 (197/24032). This frequency is about 39 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. This variant has been reported in one NF1 patient without strong evidence for causality (Wimmer_2007). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign. Taken together, this variant is classified as benign.
Invitae RCV000196969 SCV000252686 benign Neurofibromatosis, type 1 2018-01-04 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000249721 SCV000711560 benign not specified 2014-11-24 criteria provided, single submitter clinical testing Glu1423Glu in exon 32 of NF1: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue and is not located with in the splice consensus sequence. It has been identified in 0.9% (38/4406) of Af rican American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS; dbSNP rs17886566).
PreventionGenetics RCV000249721 SCV000306265 likely benign not specified criteria provided, single submitter clinical testing
PreventionGenetics RCV000679390 SCV000806281 likely benign not provided 2015-12-22 criteria provided, single submitter clinical testing

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