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

dbSNP: rs61509952

Total submissions: 12

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
PreventionGenetics, part of Exact Sciences	RCV000185816	SCV000308491	benign	not specified		criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000377067	SCV000426809	benign	Congenital hyperammonemia, type I	2016-06-14	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	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.
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000377067	SCV000744160	benign	Congenital hyperammonemia, type I	2017-05-31	criteria provided, single submitter	clinical testing
GeneDx	RCV000509330	SCV001856317	benign	not provided	2021-05-06	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000377067	SCV001876293	benign	Congenital hyperammonemia, type I	2021-07-30	criteria provided, single submitter	clinical testing
GeneDx	RCV000185816	SCV000238762	benign	not specified	2014-03-13	flagged submission	clinical testing	The variant is found in UCD-MET panel(s).
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
Clinical Genetics, Academic Medical Center	RCV000185816	SCV001919280	benign	not specified		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000185816	SCV001957535	benign	not specified		no assertion criteria provided	clinical testing