Submissions for variant NM_001173990.3(TMEM216):c.264G>A (p.Pro88=)

gnomAD frequency: 0.84043  dbSNP: rs3741265

Total submissions: 14

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
PreventionGenetics, part of Exact Sciences	RCV000114238	SCV000306946	benign	not specified		criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV001093939	SCV000372630	benign	Joubert syndrome 2	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.
Illumina Laboratory Services, Illumina	RCV000405990	SCV000372631	benign	Meckel syndrome, type 2	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.
Athena Diagnostics	RCV000114238	SCV000615815	benign	not specified	2011-08-15	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000587023	SCV000697776	benign	not provided	2016-05-02	criteria provided, single submitter	clinical testing	Variant summary: The TMEM216 c.264G>A (p.Pro88Pro) variant affects a non-conserved nucleotide, resulting in a synonymous mutation. Mutation taster predicts the variant to be a polymorphism along with 5/5 in silico tools via Alamut predicting the variant not to affect splicing. This variant is found in 104584/120784 control chromosomes (45445 homozygotes) at a frequency of 0.8658763, suggesting this variant to be the ancestral allele; therefore it is classified as Benign.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000361073	SCV001000093	benign	Familial aplasia of the vermis	2025-02-03	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV001093939	SCV001755017	benign	Joubert syndrome 2	2021-07-10	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000405990	SCV001755018	benign	Meckel syndrome, type 2	2021-07-10	criteria provided, single submitter	clinical testing
GeneDx	RCV000587023	SCV001895220	benign	not provided	2015-03-03	criteria provided, single submitter	clinical testing
Breakthrough Genomics, Breakthrough Genomics	RCV000587023	SCV005324405	benign	not provided		criteria provided, single submitter	not provided
Genetic Services Laboratory, University of Chicago	RCV000114238	SCV000147795	likely benign	not specified		no assertion criteria provided	clinical testing	Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.
Natera, Inc.	RCV001093939	SCV001461266	benign	Joubert syndrome 2	2020-09-16	no assertion criteria provided	clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000114238	SCV001743711	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000114238	SCV001965297	benign	not specified		no assertion criteria provided	clinical testing