ClinVar Miner

Submissions for variant NM_001875.5(CPS1):c.3141+15del (rs577707531)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000339021 SCV000426840 uncertain significance Congenital hyperammonemia, type I 2016-06-14 criteria provided, single submitter clinical testing
GeneDx RCV000479720 SCV000569051 likely benign not specified 2017-10-24 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.
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000513937 SCV000610055 likely benign not provided 2017-04-24 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000513937 SCV000697876 benign not provided 2017-05-14 criteria provided, single submitter clinical testing Variant summary: c.3141+15delA in CPS1 gene is an intronic change that involves a non-conserved nucleotide. 5/5 programs in Alamut predict that this do not affect a normal splicing, however no functional studies supporting this notion were published at the time of evaluation. The variant is present in the control population dataset of ExAC at frequency of 0.007693 (831/108016chrs tested), predominantly in individuals of European descent (0.01209; 715/ 59126 chrs tested), including two homozygous occurrences. The observed frequencies exceed the maximum expected allele frequency for a pathogenic variant of 0.0015%, suggesting that it is a benign polymorphism. The variant of interest has been reported as Benign by a reputable database/clinical laboratory. Taking together, based on the prevalence of this variant in general population the variant was classified as Benign.

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