Submissions for variant NM_001126049.2(KLLN):c.-1007C>G

dbSNP: rs587780001

Total submissions: 8

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Clingen PTEN Variant Curation Expert Panel, Clingen	RCV000790889	SCV000930123	likely benign	PTEN hamartoma tumor syndrome	2019-06-25	reviewed by expert panel	curation	PTEN c.-975G>C (g.89623251G>C) meets criteria to be classified as likely benign for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the "PTEN ACMG Specifications Summary" document (assertion method column). BS1: Allele frequency of 0.006 (0.6%, 21/3466 alleles) in the European (Finnish) subpopulation and 0.002 (0.2%, 30/14,976) in the European (Non-Finnish) subpopulation of the gnomAD cohort. (PMID 27535533) BP5: Variant found in multiple cases with alternate molecular basis for disease. (internal laboratory contributors SCV000187238.1, SCV000149489.5)
GeneDx	RCV000589059	SCV000149489	benign	not provided	2017-10-23	criteria provided, single submitter	clinical testing	This variant is associated with the following publications: (PMID: 25669429, 21633361)
Ambry Genetics	RCV000115580	SCV000187238	uncertain significance	Hereditary cancer-predisposing syndrome	2014-05-05	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV000252011	SCV000303566	likely benign	not specified	2018-07-09	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000589059	SCV000696555	benign	not provided	2017-05-26	criteria provided, single submitter	clinical testing	Variant summary: The PTEN c.-975G>C (also known as c.-976G>C) variant involves the alteration of a non-conserved nucleotide in 5'UTR. One in silico tool predicts a benign outcome for this variant. This variant was found in 55/30846 control chromosomes at a frequency of 0.0017831, which is approximately 285 times the estimated maximal expected allele frequency of a pathogenic PTEN variant (0.0000063), suggesting this variant is likely a benign polymorphism. Although multiple clinical diagnostic laboratories classified this variant as uncertain significance, this variant is classified as benign due to its relatively high frequency in controls.
CeGaT Center for Human Genetics Tuebingen	RCV000589059	SCV001148034	likely benign	not provided	2024-02-01	criteria provided, single submitter	clinical testing	PTEN: BS1
Sema4, Sema4	RCV000115580	SCV002528280	likely benign	Hereditary cancer-predisposing syndrome	2021-03-15	criteria provided, single submitter	curation
Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital	RCV000781947	SCV000920390	uncertain significance	Seizure	2017-08-16	no assertion criteria provided	clinical testing