Submissions for variant NM_000152.5(GAA):c.2647-20T>G

dbSNP: rs1555603208

Total submissions: 3

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Counsyl	RCV000671068	SCV000796008	uncertain significance	Glycogen storage disease, type II	2017-11-27	criteria provided, single submitter	clinical testing
Genetic Services Laboratory, University of Chicago	RCV001816675	SCV002065879	likely pathogenic	not provided	2021-09-17	criteria provided, single submitter	clinical testing	The second sequence change, c.2647-20T>G, occurs in intron 18. This variant is absent from population databases including ExAC and gnomAD. This sequence change has been reported in the compound heterozygous state with the c.-32-13T>G variant in an individual with late-onset Pompe disease (PMID: 23062590). In-silico splice prediction programs predict that this sequence change likely affects normal splicing. Experimental studies demonstrated that this sequence change creates a splice acceptor site 20 bases upstream of exon 19. This leads to an insertion of 20 bases and creates a premature stop codon after 14 bases in exon 19 (PMID: 23062590). Based on these evidences, the c.2647-20T>G variant is classified as likely pathogenic.
Mayo Clinic Laboratories, Mayo Clinic	RCV001816675	SCV004225027	likely pathogenic	not provided	2023-01-26	criteria provided, single submitter	clinical testing	PP3, PP4, PM2_supporting, PM3_supporting, PS3