Submissions for variant NM_000051.4(ATM):c.7788+8G>T

gnomAD frequency: 0.00165  dbSNP: rs112775908

Total submissions: 31

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000115256	SCV000149165	benign	not specified	2015-04-13	criteria provided, single submitter	clinical testing	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae	RCV000119166	SCV000153893	benign	Ataxia-telangiectasia syndrome	2024-02-01	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV000115256	SCV000301684	likely benign	not specified		criteria provided, single submitter	clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000115256	SCV000602565	likely benign	not specified	2017-01-03	criteria provided, single submitter	clinical testing
Color Diagnostics, LLC DBA Color Health	RCV000579980	SCV000682434	likely benign	Hereditary cancer-predisposing syndrome	2015-01-09	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000589845	SCV000694360	benign	not provided	2017-02-09	criteria provided, single submitter	clinical testing
Counsyl	RCV000119166	SCV000792935	likely benign	Ataxia-telangiectasia syndrome	2017-07-24	criteria provided, single submitter	clinical testing
Athena Diagnostics	RCV000589845	SCV000840964	benign	not provided	2018-08-17	criteria provided, single submitter	clinical testing
Eurofins Ntd Llc (ga)	RCV000115256	SCV000854937	likely benign	not specified	2018-05-29	criteria provided, single submitter	clinical testing
Mendelics	RCV000119166	SCV001138567	likely benign	Ataxia-telangiectasia syndrome	2019-05-28	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000589845	SCV001148446	uncertain significance	not provided	2024-07-01	criteria provided, single submitter	clinical testing	ATM: PM2:Supporting, BP4
Illumina Laboratory Services, Illumina	RCV000119166	SCV001261063	uncertain significance	Ataxia-telangiectasia syndrome	2017-04-27	criteria provided, single submitter	clinical testing	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	RCV001798326	SCV002042939	likely benign	Breast and/or ovarian cancer	2023-05-23	criteria provided, single submitter	clinical testing
Genetic Services Laboratory, University of Chicago	RCV000115256	SCV002071012	benign	not specified	2021-02-15	criteria provided, single submitter	clinical testing
Sema4, Sema4	RCV000579980	SCV002538193	benign	Hereditary cancer-predisposing syndrome	2020-08-21	criteria provided, single submitter	curation
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000115256	SCV002570210	likely benign	not specified	2023-08-15	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV000579980	SCV002673261	likely benign	Hereditary cancer-predisposing syndrome	2015-08-13	criteria provided, single submitter	clinical testing	This alteration is classified as likely 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.
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000589845	SCV002774005	benign	not provided	2022-09-22	criteria provided, single submitter	clinical testing
Myriad Genetics, Inc.	RCV004589578	SCV005083954	benign	Familial cancer of breast	2024-06-17	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 is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 25085752].
True Health Diagnostics	RCV000579980	SCV000886666	likely benign	Hereditary cancer-predisposing syndrome	2018-08-07	no assertion criteria provided	clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001357795	SCV001553377	likely benign	Malignant tumor of breast		no assertion criteria provided	clinical testing	ATM, EXON52, c.7788+8G>T, r.(spl)?, Heterozygous, Likely Benign The ATM c.7788+8G>T variant was not identified in the literature nor was it identified in the Cosmic, MutDB, or LOVD 3.0 databases. The variant was identified in the following databases: dbSNP (ID: rs112775908) as “With other allele”, ClinVar (as likely benign by ARUP Laboratories and PreventionGenetics, and as benign by GeneDx and Invitae), Clinvitae (as likely benign and benign). The variant was identified in control databases in 404 of 276410 chromosomes (1 homozygous) at a frequency of 0.001462 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). Observations by population include African in 7 of 24012 chromosomes (freq: 0.000292), Other in 4 of 6446 chromosomes (freq: 0.000621), Latino in 18 of 34394 chromosomes (freq: 0.000523), European (Non-Finnish) in 355 (1 homozygous) of 126082 chromosomes (freq: 0.002816), Ashkenazi Jewish in 11 of 10126 chromosomes (freq: 0.001086), and European (Finnish) in 9 of 25766 chromosomes (freq: 0.000349), while the variant was not observed in the East Asian and South Asian populations. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000589845	SCV001740244	likely benign	not provided		no assertion criteria provided	clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	RCV000589845	SCV001797407	likely benign	not provided		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center	RCV000589845	SCV001809671	likely benign	not provided		no assertion criteria provided	clinical testing
Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute	RCV000589845	SCV001906323	likely benign	not provided		no assertion criteria provided	clinical testing
Clinical Genetics, Academic Medical Center	RCV000589845	SCV001918095	likely benign	not provided		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000589845	SCV001929071	likely benign	not provided		no assertion criteria provided	clinical testing
Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.	RCV000579980	SCV001950172	likely benign	Hereditary cancer-predisposing syndrome	2021-09-15	no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000589845	SCV001957082	likely benign	not provided		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000589845	SCV001966043	likely benign	not provided		no assertion criteria provided	clinical testing
Natera, Inc.	RCV000119166	SCV002083634	likely benign	Ataxia-telangiectasia syndrome	2019-10-30	no assertion criteria provided	clinical testing