Submissions for variant NM_000038.6(APC):c.3462AGA[2] (p.Glu1157del)

dbSNP: rs386833391

Total submissions: 25

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000034412	SCV000148993	benign	not provided	2018-03-29	criteria provided, single submitter	clinical testing	This variant is associated with the following publications: (PMID: 22703879, 21488257, 24599579, 27153395, 24345752, 24113346, 29367705)
Ambry Genetics	RCV000115084	SCV000172880	benign	Hereditary cancer-predisposing syndrome	2014-12-09	criteria provided, single submitter	clinical testing	This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000144564	SCV000252584	benign	Familial adenomatous polyposis 1	2024-02-01	criteria provided, single submitter	clinical testing
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	RCV000239004	SCV000297019	benign	Familial multiple polyposis syndrome	2015-11-30	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000300515	SCV000452006	likely benign	APC-Associated Polyposis Disorders	2016-06-14	criteria provided, single submitter	clinical testing
Color Diagnostics, LLC DBA Color Health	RCV000115084	SCV000681606	benign	Hereditary cancer-predisposing syndrome	2016-03-21	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000034412	SCV000694033	benign	not provided	2016-12-05	criteria provided, single submitter	clinical testing	Variant summary: The APC c.3468_3470delAGA (p.Glu1157del) variant causes deletion of a Glutamic acid in a run of 4 repetitive Glutamic acids. This variant was found in 148/121852 control chromosomes (1 homozygote), predominantly observed in the African subpopulation at a frequency of 0.0130777 (133/10170). This frequency is about 183 times the estimated maximal expected allele frequency of a pathogenic APC variant (0.0000714), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. The variant of interest has been reported in patients with familial adenomatous polyposis including co-occurrences with other potentially pathogenic variants (Grandval_2014), supporting for the benign outcome. In addition, multiple clinical diagnostic laboratories/reputable databases have classified this variant as likely benign/benign. Taken together, this variant is classified as Benign.
Eurofins Ntd Llc (ga)	RCV000254628	SCV000703676	benign	not specified	2016-11-23	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV000254628	SCV000805395	benign	not specified	2017-05-30	criteria provided, single submitter	clinical testing
Mendelics	RCV000144564	SCV000838107	benign	Familial adenomatous polyposis 1	2018-07-02	criteria provided, single submitter	clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000034412	SCV000885022	benign	not provided	2023-06-19	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000034412	SCV000887523	benign	not provided	2022-10-21	criteria provided, single submitter	clinical testing
St. Jude Molecular Pathology, St. Jude Children's Research Hospital	RCV000144564	SCV001775520	benign	Familial adenomatous polyposis 1	2021-08-02	criteria provided, single submitter	clinical testing
Genetic Services Laboratory, University of Chicago	RCV000254628	SCV002069700	benign	not specified	2020-08-31	criteria provided, single submitter	clinical testing
Sema4, Sema4	RCV000115084	SCV002533747	benign	Hereditary cancer-predisposing syndrome	2020-08-11	criteria provided, single submitter	curation
Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.	RCV000115084	SCV004014987	benign	Hereditary cancer-predisposing syndrome	2023-05-16	criteria provided, single submitter	clinical testing
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000254628	SCV004025054	likely benign	not specified	2023-08-15	criteria provided, single submitter	clinical testing
All of Us Research Program, National Institutes of Health	RCV003996162	SCV004839815	benign	Classic or attenuated familial adenomatous polyposis	2024-02-05	criteria provided, single submitter	clinical testing	actually g.112174759_112174761del, c.3468_3470del, p.E1157del was c.3460_3462del, p.1154_1154del
Myriad Genetics, Inc.	RCV000144564	SCV004931015	likely benign	Familial adenomatous polyposis 1	2024-03-20	criteria provided, single submitter	clinical testing	This variant is considered likely benign. This variant has been observed at a population frequency that is significantly greater than expected given the associated disease prevalence and penetrance.
Biesecker Lab/Clinical Genomics Section, National Institutes of Health	RCV000034412	SCV000043122	variant of unknown significance	not provided	2012-07-13	no assertion criteria provided	research	Converted during submission to Uncertain significance.
Pathway Genomics	RCV000144564	SCV000189856	likely benign	Familial adenomatous polyposis 1	2014-07-24	no assertion criteria provided	clinical testing
True Health Diagnostics	RCV000115084	SCV000693478	likely benign	Hereditary cancer-predisposing syndrome	2017-10-25	no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center	RCV000254628	SCV001807977	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics, Academic Medical Center	RCV000034412	SCV001924114	likely benign	not provided		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000254628	SCV001927045	benign	not specified		no assertion criteria provided	clinical testing