Submissions for variant NM_001184.4(ATR):c.1326A>G (p.Lys442=)

gnomAD frequency: 0.01766  dbSNP: rs28897765

Total submissions: 9

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Genetic Services Laboratory, University of Chicago	RCV000145288	SCV000192365	benign	not specified	2013-02-08	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000365738	SCV000441453	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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000588029	SCV000697771	benign	not provided	2016-04-27	criteria provided, single submitter	clinical testing	Variant summary: The c.1326A>G variant affects a non-conserved nucleotide, resulting in a synonymous mutation. Mutation taster predicts benign outcome for this variant along with 4/5 in silico tools via Alamut predicting the variant not to have an impact on normal splicing. This variant is found in 2299/121410 control chromosomes (48 homozygotes) at a frequency of 0.0189358, which is about 30297 times of the maximal expected frequency of a pathogenic allele (0.0000006), suggesting this variant is benign. In addition, a clinical laboratory classifies this variant as benign (without evidence to independently evaluate). Taken together, this variant was classified as Benign.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000588029	SCV001470807	benign	not provided	2023-11-02	criteria provided, single submitter	clinical testing
Invitae	RCV000588029	SCV001725422	benign	not provided	2024-02-01	criteria provided, single submitter	clinical testing
GeneDx	RCV000588029	SCV001944569	benign	not provided	2015-03-03	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000365738	SCV003801898	benign	Seckel syndrome 1	2023-02-08	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV003126510	SCV003801899	benign	Familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome	2023-02-08	criteria provided, single submitter	clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center	RCV003126510	SCV004015545	benign	Familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome	2023-07-07	criteria provided, single submitter	clinical testing