Submissions for variant NM_000290.4(PGAM2):c.415-3C>T

gnomAD frequency: 0.00048  dbSNP: rs201133395

Total submissions: 3

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV001719002	SCV000724874	likely benign	not provided	2020-08-06	criteria provided, single submitter	clinical testing
Labcorp Genetics (formerly Invitae), Labcorp	RCV001349366	SCV001543708	uncertain significance	Glycogen storage disease type X	2022-10-17	criteria provided, single submitter	clinical testing	This sequence change falls in intron 1 of the PGAM2 gene. It does not directly change the encoded amino acid sequence of the PGAM2 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs201133395, gnomAD 0.09%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with PGAM2-related conditions. ClinVar contains an entry for this variant (Variation ID: 513506). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
CeGaT Center for Human Genetics Tuebingen	RCV001719002	SCV004156816	likely benign	not provided	2023-02-01	criteria provided, single submitter	clinical testing	PGAM2: BP4