Total submissions: 13
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Eurofins Ntd Llc |
RCV000078161 | SCV000109999 | benign | not specified | 2017-05-03 | criteria provided, single submitter | clinical testing | |
Prevention |
RCV000078161 | SCV000302667 | benign | not specified | criteria provided, single submitter | clinical testing | ||
Illumina Laboratory Services, |
RCV000353996 | SCV000407284 | benign | Glycogen storage disease, type II | 2018-03-06 | 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. |
Center for Pediatric Genomic Medicine, |
RCV000431108 | SCV000510579 | benign | not provided | 2016-11-04 | criteria provided, single submitter | clinical testing | |
Gene |
RCV000431108 | SCV000521131 | benign | not provided | 2018-01-04 | criteria provided, single submitter | clinical testing | This variant is associated with the following publications: (PMID: 9266392, 21644219, 18301443, 14643388, 17805474, 28725570) |
Invitae | RCV000353996 | SCV000626522 | other | Glycogen storage disease, type II | 2018-12-31 | criteria provided, single submitter | clinical testing | |
Women's Health and Genetics/Laboratory Corporation of America, |
RCV000431108 | SCV000695646 | benign | not provided | 2017-05-03 | criteria provided, single submitter | clinical testing | Variant summary: The GAA c.1726G>A (p.Gly576Ser) variant involves the alteration of a conserved nucleotide resulting in a missense substitution in the glycoside hydrolase superfamily domain (InterPro). 4/4 in silico tools predict a damaging outcome for this variant. This variant was found in the large control database ExAC in 2266 of 121736 control chromosomes (124 homozygotes) from all ethnicities, but was predominantly observed in the East Asian subpopulation at a frequency of 0.144416 (1244/8614; 109 homozygotes). This frequency is about 34 times the estimated maximal expected allele frequency of a pathogenic GAA variant (0.0042205), strongly suggesting this is likely a benign polymorphism found primarily in the populations of East Asian origin. This variant and its haplotype complex, p.[G576S; E689K], are widely regarded as a variant causing pseudodeficiency of alfa-glucosidase. The subjects who carried the p.[G576S;E689K] in homozygous state or compound heterozygous state with a truncating variant were not found to clinically manifest Pompe disease, yet they had a reduced enzymatic activity (Kroos_EJHG_2008). In addition, this variant has also been found in cis with two known pathogenic variants (p. Asp645Glu and p.Trp746Cys) in patients with Pompe disease (Yang_MGM_2011), strongly suggesting for a benign outcome. In vitro functional studies are consistent with this variant being a functional polymorphism; this variant maintains a residual activity and it can significantly reduce the functional activity of a potentially pathogenic variant when found in cis (Pipo_Peditr Neurol_2003; Yang_MGM_2011). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign. |
ARUP Laboratories, |
RCV000353996 | SCV001158935 | benign | Glycogen storage disease, type II | 2023-10-26 | criteria provided, single submitter | clinical testing | |
Ambry Genetics | RCV003298132 | SCV003989440 | benign | Cardiovascular phenotype | 2023-03-30 | criteria provided, single submitter | clinical testing | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. |
Baylor Genetics | RCV000353996 | SCV004195413 | pathogenic | Glycogen storage disease, type II | 2024-03-30 | criteria provided, single submitter | clinical testing | |
Genetic Services Laboratory, |
RCV000078161 | SCV000151252 | likely benign | not specified | no assertion criteria provided | clinical testing | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. | |
Genome |
RCV000353996 | SCV001749549 | not provided | Glycogen storage disease, type II | no assertion provided | phenotyping only | Variant interpreted as Benign and reported on 03-18-2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. | |
Gene |
RCV000353996 | SCV001761182 | not provided | Glycogen storage disease, type II | no assertion provided | literature only | Pseudodeficiency allele c.1726 G>A (p.Gly576Ser), which interferes with enzyme activity toward artificial substrates, is relatively common in Asian as well as other populations studied as part of newborn screening programs. |