ClinVar Miner

Submissions for variant NM_002617.4(PEX10):c.291A>G (p.Thr97=)

gnomAD frequency: 0.73859  dbSNP: rs2494598
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000117902 SCV000316393 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services,Illumina RCV000326499 SCV000355615 benign Peroxisome biogenesis disorder 6A (Zellweger) 2018-01-13 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000117902 SCV000917984 benign not specified 2017-10-09 criteria provided, single submitter clinical testing Variant summary: The PEX10 c.291A>G (p.Thr97Thr) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change located in the Pex, N-terminal domain(IPR006845) (InterPro). One in silico tool predicts a benign 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 212895/276368 control chromosomes (82611 homozygotes) (gnomAD) at a frequency of 0.7703316, indicating this variant is the major allele. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign. Taken together, this variant is classified as benign.
GeneDx RCV000676046 SCV000981986 benign not provided 2018-06-13 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 RCV001523636 SCV001733383 benign Peroxisome biogenesis disorder, complementation group 7 2020-12-05 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000326499 SCV001754748 benign Peroxisome biogenesis disorder 6A (Zellweger) 2021-07-08 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001537790 SCV001754749 benign Peroxisome biogenesis disorder 6B 2021-07-08 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000117902 SCV000152177 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.
Mayo Clinic Laboratories,Mayo Clinic RCV000676046 SCV000801780 benign not provided 2015-10-21 no assertion criteria provided clinical testing
Natera, Inc. RCV001273140 SCV001455745 benign Zellweger spectrum disorders 2020-09-16 no assertion criteria provided clinical testing

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