ClinVar Miner

Submissions for variant NM_000282.4(PCCA):c.1429+7A>G

gnomAD frequency: 0.01356  dbSNP: rs16957276
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000174996 SCV000226413 benign not specified 2015-01-13 criteria provided, single submitter clinical testing
Preventiongenetics, part of Exact Sciences RCV000174996 SCV000303451 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000370381 SCV000382016 likely benign Propionic acidemia 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
GeneDx RCV000174996 SCV000514037 benign not specified 2018-03-05 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 RCV000174996 SCV000917966 benign not specified 2018-01-05 criteria provided, single submitter clinical testing Variant summary: The PCCA c.1429+7A>G variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a benign outcome for this variant. 4/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 4420/277054 control chromosomes (51 homozygotes) at a frequency of 0.0159536, which is approximately 5 times the estimated maximal expected allele frequency of a pathogenic PCCA variant (0.003446), suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000370381 SCV001159143 benign Propionic acidemia 2021-11-26 criteria provided, single submitter clinical testing
Invitae RCV000370381 SCV001728431 benign Propionic acidemia 2024-02-01 criteria provided, single submitter clinical testing
Natera, Inc. RCV000370381 SCV001455849 benign Propionic acidemia 2020-09-16 no assertion criteria provided clinical testing

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