Submissions for variant NM_000038.6(APC):c.1958+8T>C

gnomAD frequency: 0.00510  dbSNP: rs62626346

Total submissions: 19

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000077982	SCV000109813	benign	not specified	2012-10-26	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV000077982	SCV000301589	benign	not specified		criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000379464	SCV000451993	benign	APC-Associated Polyposis Disorders	2018-01-13	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.
Invitae	RCV003315584	SCV000562613	benign	Familial adenomatous polyposis 1	2024-02-01	criteria provided, single submitter	clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV001610343	SCV000602529	benign	not provided	2023-10-23	criteria provided, single submitter	clinical testing
Color Diagnostics, LLC DBA Color Health	RCV000579978	SCV000681498	benign	Hereditary cancer-predisposing syndrome	2016-03-21	criteria provided, single submitter	clinical testing
GeneDx	RCV001610343	SCV001840718	benign	not provided	2015-03-03	criteria provided, single submitter	clinical testing
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000077982	SCV002550591	benign	not specified	2023-08-15	criteria provided, single submitter	clinical testing
Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.	RCV000579978	SCV002819226	benign	Hereditary cancer-predisposing syndrome	2022-11-22	criteria provided, single submitter	clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center	RCV003315584	SCV004015759	benign	Familial adenomatous polyposis 1	2023-07-07	criteria provided, single submitter	clinical testing
Myriad Genetics, Inc.	RCV003315584	SCV004931024	benign	Familial adenomatous polyposis 1	2024-03-07	criteria provided, single submitter	clinical testing	This variant is considered benign. This variant is intronic and is not expected to impact mRNA splicing. This variant has been observed at a population frequency that is significantly greater than expected given the associated disease prevalence and penetrance.
Systems Biology Platform Zhejiang California International NanoSystems Institute	RCV000073605	SCV000105196	cancer	Familial colorectal cancer		no assertion criteria provided	not provided	Converted during submission to other.
Mayo Clinic Laboratories, Mayo Clinic	RCV000077982	SCV000256935	benign	not specified		no assertion criteria provided	clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001353873	SCV000591100	benign	Carcinoma of colon		no assertion criteria provided	clinical testing	The c.1958+8T>C variant has been reported once in the InSiGHT database in an individual with familial adenomatous polyposis. It is listed in the dbSNP database (rs#:62626346) and reported from the 1000 genomes project (frequency: 0.026) and in a Chinese and Japanese cohort (frequency: 0.067) as well as the exome variant server as a low frequency variant increasing the likelihood this variant does not have clinical significance. The variant is located in the 5' splice region but does not affect the highly conserved +1 and +2 positions. In summary, based on above information this variant meets our laboratory's criteria to be classified benign.
True Health Diagnostics	RCV000579978	SCV000693472	likely benign	Hereditary cancer-predisposing syndrome	2017-09-29	no assertion criteria provided	clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	RCV000077982	SCV001797967	benign	not specified		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center	RCV000077982	SCV001808058	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics, Academic Medical Center	RCV000077982	SCV001924958	benign	not specified		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000077982	SCV001952726	benign	not specified		no assertion criteria provided	clinical testing