Submissions for variant NM_001173990.3(TMEM216):c.432-1G>C

dbSNP: rs10897158

Total submissions: 13

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Genetic Services Laboratory, University of Chicago	RCV000114239	SCV000147796	benign	not specified	2013-09-04	criteria provided, single submitter	clinical testing
Eurofins Ntd Llc (ga)	RCV000114239	SCV000203634	benign	not specified	2014-04-25	criteria provided, single submitter	clinical testing
Invitae	RCV000200066	SCV000252759	benign	Familial aplasia of the vermis	2024-02-01	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV000114239	SCV000306948	benign	not specified		criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV001093993	SCV000372642	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	RCV000291379	SCV000372643	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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000590397	SCV000697778	benign	not provided	2016-05-02	criteria provided, single submitter	clinical testing	Variant summary: The variant of interest, c.432-1G>C, is located at a non-conserved intronic position in intron 4, at the extreme 3'-end of the TMEM216 gene. However, exon 5, the last exon, contains only 1 amino acid before the stop codon. Alamut predicts the loss of a splice sight by 4/5 in silico programs, 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 95665/117336 (including 40102 homozygotes) indicating that the variant of interest is the major allele (most commonly observed in the general population). In addition, multiple reputable clinical laboratories/databases with a classification of "benign." Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as Benign.
Mendelics	RCV000988565	SCV001138331	benign	Joubert syndrome 1	2019-05-28	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV001093993	SCV001755019	benign	Joubert syndrome 2	2021-07-10	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000291379	SCV001755020	benign	Meckel syndrome, type 2	2021-07-10	criteria provided, single submitter	clinical testing
GeneDx	RCV000590397	SCV001758257	benign	not provided	2015-03-03	criteria provided, single submitter	clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000114239	SCV001741553	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000114239	SCV001974330	benign	not specified		no assertion criteria provided	clinical testing