ClinVar Miner

Submissions for variant NM_000303.3(PMM2):c.324G>A (p.Ala108=)

gnomAD frequency: 0.01239  dbSNP: rs62031146
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics,Children's Hospital of Philadelphia RCV000117997 SCV000257665 benign not specified 2015-06-17 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000117997 SCV000303550 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services,Illumina RCV000554451 SCV000399671 benign PMM2-congenital disorder of glycosylation 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
GeneDx RCV000117997 SCV000517828 benign not specified 2016-02-23 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.
Invitae RCV000554451 SCV000633724 benign PMM2-congenital disorder of glycosylation 2021-12-18 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000117997 SCV000920010 benign not specified 2017-09-25 criteria provided, single submitter clinical testing Variant summary: The PMM2 c.324G>A (p.Ala108Ala) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE site of SRp55. However, these predictions have yet to be confirmed by functional studies. This variant was found in 2137/121286 control chromosomes at a frequency of 0.0176195, which is approximately 3 times the estimated maximal expected allele frequency of a pathogenic PMM2 variant (0.0055902), suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign.
Genetic Services Laboratory,University of Chicago RCV000117997 SCV000152315 likely benign not specified no assertion criteria provided clinical testing Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000554451 SCV000733547 benign PMM2-congenital disorder of glycosylation no assertion criteria provided clinical testing
Natera, Inc. RCV000554451 SCV001457167 benign PMM2-congenital disorder of glycosylation 2020-09-16 no assertion criteria provided clinical testing
Clinical Genetics, Academic Medical Center RCV000117997 SCV001922761 benign not specified no assertion criteria provided clinical testing

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