ClinVar Miner

Submissions for variant NM_000267.3(NF1):c.3270A>C (p.Gly1090=) (rs150015024)

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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 RCV000163445 SCV000213992 likely benign Hereditary cancer-predisposing syndrome 2014-11-04 criteria provided, single submitter clinical testing
GeneDx RCV000252563 SCV000726312 likely benign not specified 2017-12-28 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 RCV000252563 SCV000919889 benign not specified 2018-10-19 criteria provided, single submitter clinical testing Variant summary: NF1 c.3270A>C alters a non-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 allele was found at a frequency of 0.00021 in 276484 control chromosomes, predominantly at a frequency of 0.0023 within the African subpopulation in the gnomAD database. The observed variant frequency within African control individuals in the gnomAD database is approximately 11-fold of 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 African origin. To our knowledge, no occurrence of c.3270A>C in individuals affected with Neurofibromatosis Type 1 and no experimental evidence demonstrating its impact on protein function have been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign.
Invitae RCV000204634 SCV000259909 benign Neurofibromatosis, type 1 2018-01-09 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000252563 SCV000711559 benign not specified 2014-11-24 criteria provided, single submitter clinical testing Gly1090Gly in exon 25 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 1.4% (7/492) of Afri can chromosomes from a broad population by the 1000 Genomes Project (http://www. ncbi.nlm.nih.gov/projects/SNP; dbSNP rs150015024).
PreventionGenetics RCV000252563 SCV000306254 likely benign not specified criteria provided, single submitter clinical testing

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