Submissions for variant NM_005634.3(SOX3):c.157G>C (p.Val53Leu)

gnomAD frequency: 0.00403  dbSNP: rs200361128

Total submissions: 12

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000153990	SCV000203615	likely benign	not specified	2014-06-29	criteria provided, single submitter	clinical testing
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine	RCV000454344	SCV000537978	likely pathogenic	Abnormal brain morphology		criteria provided, single submitter	research
Ambry Genetics	RCV000720991	SCV000851875	benign	History of neurodevelopmental disorder	2012-12-03	criteria provided, single submitter	clinical testing	This alteration is classified as benign based on a combination of the following: 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.
Invitae	RCV000878811	SCV001021783	benign	not provided	2024-01-15	criteria provided, single submitter	clinical testing
Genetic Services Laboratory, University of Chicago	RCV000153990	SCV002066086	likely benign	not specified	2019-03-18	criteria provided, single submitter	clinical testing
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000153990	SCV004847355	benign	not specified	2023-10-18	criteria provided, single submitter	clinical testing	The p.Val53Leu variant in SOX3 is classified as benign because it has been identified in 2.1% of African/African American chromosomes, including 1 homozygote, in gnomAD (http://gnomad.broadinstitute.org, v.3.1.2), which is higher than expected for a disease causing variant in SOX3. ACMG/AMP Criteria applied: BA1.
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	RCV004593993	SCV005086758	likely benign	Intellectual disability, X-linked, with panhypopituitarism	2023-07-17	criteria provided, single submitter	clinical testing	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as likely benign. Following criteria are met: 0308 - Population frequency for this variant is out of keeping with known incidence of intellectual developmental disorder, X-linked, with isolated growth hormone deficiency, with more than 300 hemizygous alleles in gnomAD v2 (MIM#300123). (SB) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000153990	SCV001740656	benign	not specified		no assertion criteria provided	clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	RCV000878811	SCV001797719	likely benign	not provided		no assertion criteria provided	clinical testing
Clinical Genetics, Academic Medical Center	RCV000153990	SCV001925375	benign	not specified		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000878811	SCV001932787	likely benign	not provided		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000153990	SCV001969360	benign	not specified		no assertion criteria provided	clinical testing