Submissions for variant NM_001160372.4(TRAPPC9):c.2811-4G>A

gnomAD frequency: 0.00004  dbSNP: rs374826041

Total submissions: 5

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Illumina Laboratory Services, Illumina	RCV000270490	SCV000472174	likely benign	Intellectual disability, autosomal recessive 13	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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Ambry Genetics	RCV002317858	SCV000849724	uncertain significance	Inborn genetic diseases	2019-11-20	criteria provided, single submitter	clinical testing	The c.3105-4G>A intronic variant results from a G to A substitution 4 nucleotides upstream from coding exon 20 in the TRAPPC9 gene. This nucleotide position is poorly conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is not predicted to have any significant effect on this splice acceptor site; however, direct evidence is unavailable. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
CeGaT Center for Human Genetics Tuebingen	RCV001311334	SCV001501478	likely benign	not provided	2020-09-01	criteria provided, single submitter	clinical testing
Invitae	RCV001311334	SCV004305594	benign	not provided	2023-11-28	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV003912551	SCV004728782	likely benign	TRAPPC9-related condition	2019-05-08	criteria provided, single submitter	clinical testing	This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).