ClinVar Miner

Submissions for variant NM_001875.5(CPS1):c.2679C>G (p.Gly893=) (rs2287599)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000116831 SCV000168025 benign not specified 2013-07-25 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.
PreventionGenetics,PreventionGenetics RCV000116831 SCV000308497 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000347604 SCV000426837 benign Congenital hyperammonemia, type I 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.
Integrated Genetics/Laboratory Corporation of America RCV000509201 SCV000697874 benign not provided 2017-05-14 criteria provided, single submitter clinical testing Variant summary: The CPS1 c.2679C>G (p.Gly893Gly) variant involves the alteration of a non-conserved nucleotide causing a synonymous change that 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may remove ESE binding sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 71012/121158 control chromosomes (21467 homozygotes) at a frequency of 0.5861107, which is approximately 371 times the estimated maximal expected allele frequency of a pathogenic CPS1 variant (0.0015811) and indicates that the variant is the major allele (the allele most commonly seen in the general population). Therefore, suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as "likely benign/benign." Therefore, the variant of interest has been classified as Benign.
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center RCV000347604 SCV000744166 benign Congenital hyperammonemia, type I 2017-06-28 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000116831 SCV000150905 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.
GenomeConnect, ClinGen RCV000509201 SCV000607291 not provided not provided no assertion provided phenotyping only GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen RCV000347604 SCV000734169 benign Congenital hyperammonemia, type I no assertion criteria provided clinical testing

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