ClinVar Miner

Submissions for variant NM_000244.3(MEN1):c.-20G>A (rs386134244)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Integrated Genetics/Laboratory Corporation of America RCV000480991 SCV000052856 benign not specified 2018-09-12 criteria provided, single submitter clinical testing Variant summary: MEN1 c.-20G>A is located in the untranslated mRNA region upstream of the initiation codon. The variant allele was found at a frequency of 0.00066 in 145114 control chromosomes, predominantly at a frequency of 0.006 within the African subpopulation in the gnomAD database. The observed variant frequency within African control individuals in the gnomAD database is approximately 288 fold of the estimated maximal expected allele frequency for a pathogenic variant in MEN1 causing Multiple Endocrine Neoplasia Type 1 phenotype (2.1e-05), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African origin. To our knowledge, no occurrence of c.-20G>A in individuals affected with Multiple Endocrine Neoplasia Type 1 and no experimental evidence demonstrating its impact on protein function have been reported. Two 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.
Counsyl RCV000030190 SCV000487916 likely benign Multiple endocrine neoplasia, type 1 2015-12-01 criteria provided, single submitter clinical testing
GeneDx RCV000480991 SCV000565124 likely benign not specified 2017-12-01 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.

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