Submissions for variant NM_001184.4(ATR):c.3120G>A (p.Leu1040=)

dbSNP: rs28910272

Total submissions: 9

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Genetic Services Laboratory, University of Chicago	RCV000145301	SCV000192378	benign	not specified	2013-07-02	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000327853	SCV000441438	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	RCV000589121	SCV000697783	benign	not provided	2016-04-28	criteria provided, single submitter	clinical testing	Variant summary: The variant of interest causes a synonymous change involving a conserved nucleotide with 4/5 in silico programs via Alamut predicting an effect on splicing, although these predictions have yet to be functionally assessed. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 2205/111476 (1/50 including 40 homozygotes), which exceeds the predicted maximum expected allele frequency for a pathogenic ATR variant of 1/1666666. In addition, a reputable clinical laboratory cites the variant as "benign." Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as Benign.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000589121	SCV001473769	benign	not provided	2023-11-02	criteria provided, single submitter	clinical testing
Invitae	RCV000589121	SCV001725419	benign	not provided	2024-02-01	criteria provided, single submitter	clinical testing
GeneDx	RCV000589121	SCV001739043	benign	not provided	2015-03-03	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000327853	SCV003801699	benign	Seckel syndrome 1	2023-02-08	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV003126518	SCV003801700	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	RCV003126518	SCV004015490	benign	Familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome	2023-07-07	criteria provided, single submitter	clinical testing