Submissions for variant NM_001184.4(ATR):c.7875G>A (p.Gln2625=)

gnomAD frequency: 0.88595  dbSNP: rs1802904

Total submissions: 11

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000079601	SCV000111483	benign	not specified	2013-05-09	criteria provided, single submitter	clinical testing
Genetic Services Laboratory, University of Chicago	RCV000079601	SCV000192411	likely benign	not specified	2013-04-25	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000366216	SCV000441390	benign	Seckel syndrome 1	2018-01-12	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.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000079601	SCV000538376	benign	not specified	2016-03-28	criteria provided, single submitter	clinical testing	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000588079	SCV000697788	benign	not provided	2016-04-26	criteria provided, single submitter	clinical testing	Variant summary: The c.7875G>A variant affects a non-conserved nucleotide, resulting in a synonymous change. Mutation taster predicts polymorphism outcome for this variant. 3/5 programs in Alamut predict that this variant does not affect normal splicing. ESE finder predicts changes of binding motifs for splicing enhancers. However, these predictions are not confirmed by experimental studies. This variant is found in 104951/121386 control chromosomes (45665 homozygotes) at a frequency of 0.8646055, which is about 1383368 times of the maximal expected frequency of a pathogenic allele (0.0000006) in this gene. Taking together, based on the prevalence of this variant in general population the variant was classified as Benign.
Invitae	RCV000588079	SCV001729232	benign	not provided	2024-02-01	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000366216	SCV001775060	benign	Seckel syndrome 1	2021-07-14	criteria provided, single submitter	clinical testing
GeneDx	RCV000588079	SCV001944573	benign	not provided	2015-03-03	criteria provided, single submitter	clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center	RCV003315604	SCV004015468	benign	Familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome	2023-07-07	criteria provided, single submitter	clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000079601	SCV001742135	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000079601	SCV001973531	benign	not specified		no assertion criteria provided	clinical testing