Submissions for variant NM_032316.3(NICN1):c.*2328C>T

gnomAD frequency: 0.00004  dbSNP: rs386833677

Total submissions: 5

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Invitae	RCV000049637	SCV001401298	pathogenic	Non-ketotic hyperglycinemia	2023-03-27	criteria provided, single submitter	clinical testing	For these reasons, this variant has been classified as Pathogenic. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 56225). This variant has been observed in individual(s) with glycine encephalopathy (PMID: 19299230, 27362913). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant occurs in a non-coding region of the AMT gene. It does not change the encoded amino acid sequence of the AMT protein.
Myriad Genetics, Inc.	RCV000049637	SCV002060041	uncertain significance	Non-ketotic hyperglycinemia	2021-11-18	criteria provided, single submitter	clinical testing	NM_000481.3(AMT):c.-55C>T is a non coding variant classified as a variant of uncertain significance in the context of glycine encephalopathy, AMT-related. c.-55C>T has been observed in cases with relevant disease (PMID: 27362913, 19299230). Functional assessments of this variant are not available in the literature. c.-55C>T has been observed in population frequency databases (gnomAD: OTH 0.017%). In summary, there is insufficient evidence to classify NM_000481.3(AMT):c.-55C>T as pathogenic or benign. Please note: this variant was assessed in the context of healthy population screening.
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille	RCV002273949	SCV002558909	pathogenic	Neurodevelopmental delay		criteria provided, single submitter	clinical testing
Baylor Genetics	RCV000049637	SCV004196841	pathogenic	Non-ketotic hyperglycinemia	2023-03-11	criteria provided, single submitter	clinical testing
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM)	RCV000049637	SCV000082044	probable-pathogenic	Non-ketotic hyperglycinemia		no assertion criteria provided	not provided	Converted during submission to Likely pathogenic.