ClinVar Miner

Submissions for variant NM_001875.5(CPS1):c.-4_-3insTTC (rs61509952)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000185816 SCV000238762 benign not specified 2014-03-13 criteria provided, single submitter clinical testing The variant is found in UCD-MET panel(s).
PreventionGenetics,PreventionGenetics RCV000185816 SCV000308491 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000377067 SCV000426809 benign Congenital hyperammonemia, type I 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000509330 SCV000697877 benign not provided 2017-05-14 criteria provided, single submitter clinical testing Variant summary: The CPS1 c.-4_-3insTTC variant (also known as c.15_16insTTC based upon NM_001122633.2) involves the alteration of a 5' UTR nucleotide that 4/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant will not affect ESE binding. However, these predictions have yet to be confirmed by functional studies. This variant was found in 52532/120770 control chromosomes (11669 homozygotes) at a frequency of 0.4349756, which is approximately 275 times the estimated maximal expected allele frequency of a pathogenic CPS1 variant (0.0015811). Therefore, suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as "likely benign/benign." Taken together, this variant is classified as benign.
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center RCV000377067 SCV000744160 benign Congenital hyperammonemia, type I 2017-05-31 criteria provided, single submitter clinical testing
GenomeConnect, ClinGen RCV000509330 SCV000607289 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 RCV000377067 SCV000734166 benign Congenital hyperammonemia, type I no assertion criteria provided clinical testing
SingHealth Duke-NUS Institute of Precision Medicine RCV000377067 SCV000853177 likely benign Congenital hyperammonemia, type I 2017-06-07 no assertion criteria provided curation

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