Submissions for variant NM_003982.4(SLC7A7):c.1527A>G (p.Lys509=)

gnomAD frequency: 0.77937  dbSNP: rs1061040

Total submissions: 11

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000128147	SCV000171739	benign	not specified	2013-07-25	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.
Illumina Laboratory Services, Illumina	RCV000398235	SCV000385466	benign	Lysinuric protein intolerance	2018-01-13	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.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000398235	SCV001719822	benign	Lysinuric protein intolerance	2024-02-01	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000398235	SCV001755033	benign	Lysinuric protein intolerance	2021-07-10	criteria provided, single submitter	clinical testing
Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan	RCV000128147	SCV004232922	benign	not specified	2024-01-24	criteria provided, single submitter	clinical testing	This variant is classified as Benign based on local population frequency. This variant was detected in 100% of patients studied by a panel of primary immunodeficiencies. Number of patients: 95. Only high quality variants are reported.
Breakthrough Genomics, Breakthrough Genomics	RCV001824629	SCV005232739	benign	not provided		criteria provided, single submitter	not provided
Natera, Inc.	RCV000398235	SCV001455853	benign	Lysinuric protein intolerance	2020-09-16	no assertion criteria provided	clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000128147	SCV001740546	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics, Academic Medical Center	RCV000128147	SCV001922596	benign	not specified		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000128147	SCV001956229	benign	not specified		no assertion criteria provided	clinical testing
GenomeConnect, ClinGen	RCV001824629	SCV002074756	not provided	not provided		no assertion provided	phenotyping only	Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing.