ClinVar Miner

Submissions for variant NM_133259.4(LRPPRC):c.2629+18A>G

dbSNP: rs572783698
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000616953 SCV000715171 likely benign not specified 2017-02-01 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000616953 SCV004038523 benign not specified 2023-08-09 criteria provided, single submitter clinical testing Variant summary: LRPPRC c.2629+18A>G alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 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 0.00018 in 250098 control chromosomes, predominantly at a frequency of 0.0014 within the South Asian subpopulation in the gnomAD database. The observed variant frequency within South Asian control individuals in the gnomAD database is approximately 3 fold of the estimated maximal expected allele frequency for a pathogenic variant in LRPPRC causing Leigh Syndrome, French-Canadian Type phenotype (0.0005), strongly suggesting that the variant is a benign polymorphism found primarily in populations of South Asian origin. To our knowledge, no occurrence of c.2629+18A>G in individuals affected with Leigh Syndrome, French-Canadian Type and no experimental evidence demonstrating its impact on protein function have been reported. One submitter has cited clinical-significance assessments for this variant to ClinVar after 2014 and has classified the variant as likely benign. Based on the evidence outlined above, the variant was classified as benign.
Invitae RCV003558455 SCV004305929 likely benign not provided 2024-01-26 criteria provided, single submitter clinical testing

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