Submissions for variant NM_025216.3(WNT10A):c.493G>A (p.Gly165Arg)

gnomAD frequency: 0.00755  dbSNP: rs77583146

Total submissions: 12

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Illumina Laboratory Services, Illumina	RCV000346906	SCV000427544	benign	Odonto-onycho-dermal dysplasia	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.
Illumina Laboratory Services, Illumina	RCV000406139	SCV000427545	likely benign	Tooth agenesis, selective, 4	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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Illumina Laboratory Services, Illumina	RCV000283655	SCV000427546	benign	SchC6pf-Schulz-Passarge syndrome	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.
GeneDx	RCV000521785	SCV000616917	uncertain significance	not provided	2023-05-08	criteria provided, single submitter	clinical testing	Observed in the heterozygous state or as compound heterozygous with another variant in the WNT10A gene in both individuals with oligodontia as well as in unaffected individuals, and was reported as a polymorphism (Bohring et al., 2009; Yang et al., 2015; Mostowska et al., 2015); Observed in individuals with tooth agenesis in published literature who had variants in other genes associated with ectodermal anomalies (Arte et al., 2013); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 33311554, 19559398, 25545742, 30426266, 23991204, 25629078, 30555066, 31798653, 36250548)
Labcorp Genetics (formerly Invitae), Labcorp	RCV001083663	SCV000638468	benign	Odonto-onycho-dermal dysplasia; Tooth agenesis, selective, 4	2024-01-31	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000346906	SCV001737288	likely benign	Odonto-onycho-dermal dysplasia	2021-06-10	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000283655	SCV001806351	uncertain significance	SchC6pf-Schulz-Passarge syndrome	2021-07-22	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000406139	SCV001806352	uncertain significance	Tooth agenesis, selective, 4	2021-07-22	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000521785	SCV004151410	benign	not provided	2023-10-01	criteria provided, single submitter	clinical testing	WNT10A: BS1, BS2
Yale Center for Mendelian Genomics, Yale University	RCV000845116	SCV000987052	uncertain significance	Tooth agenesis	2014-09-15	no assertion criteria provided	literature only
Natera, Inc.	RCV000283655	SCV001452692	benign	SchC6pf-Schulz-Passarge syndrome	2019-12-30	no assertion criteria provided	clinical testing
PreventionGenetics, part of Exact Sciences	RCV004530358	SCV004744563	benign	WNT10A-related disorder	2020-12-18	no assertion criteria provided	clinical testing	This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).