Total submissions: 16
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Clin |
RCV000578107 | SCV001443319 | benign | Glycogen storage disease, type II | 2020-05-19 | reviewed by expert panel | curation | The highest continental population minor allele frequency for c.858+7_858+8insAGCGGGC in gnomAD v.2.1.1 is 0.7353 in the European non-Finnish population. This allele frequency is higher than the ClinGen LSD VCEP's BA1 threshold (>0.01), meeting this criterion. Note that the minor allele frequency is even higher in the Ashkenazi Jewish (0.7783) and European Finnish (0.7613) populations. There is a ClinVar entry for this variant (Variation ID: 92489, 2 star review status), with 10 submitters all classifying the variant as benign. In summary, this variant meets the criteria to be classified as benign for Pompe disease. GAA-specific ACMG/AMP criteria applied, as specified by the ClinGen LSD VCEP: BA1. |
Eurofins Ntd Llc |
RCV000078186 | SCV000110024 | benign | not specified | 2018-09-04 | criteria provided, single submitter | clinical testing | |
Genetic Services Laboratory, |
RCV000078186 | SCV000247443 | benign | not specified | 2015-08-03 | criteria provided, single submitter | clinical testing | |
Prevention |
RCV000078186 | SCV000302699 | benign | not specified | criteria provided, single submitter | clinical testing | ||
Phosphorus, |
RCV000578107 | SCV000679771 | benign | Glycogen storage disease, type II | 2017-08-01 | criteria provided, single submitter | clinical testing | |
Women's Health and Genetics/Laboratory Corporation of America, |
RCV000588321 | SCV000695667 | benign | not provided | 2017-08-21 | criteria provided, single submitter | clinical testing | Variant summary: The GAA c.858+7_858+8insAGCGGGC variant involves insertion of 7 nucleotides in an intronic location, which 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 179851/270478 control chromosomes (3918 homozygotes) at a frequency of 0.6649376, which is approximately 158 times the estimated maximal expected allele frequency of a pathogenic GAA variant (0.0042205). The observed allele frequency indicates the variant of interest is the major allele observed in the general population. In addition, the region is indicated to be highly polymorphic in gnomAD. A publication cites the variant to co-occur in an affected individual that carried two pathogenic variants. Furthermore, multiple clinical diagnostic laboratories classified this variant as benign. Taken together, this variant is classified as benign. |
Gene |
RCV000588321 | SCV000728468 | benign | not provided | 2018-06-11 | criteria provided, single submitter | clinical testing | |
Labcorp Genetics |
RCV000578107 | SCV000752093 | benign | Glycogen storage disease, type II | 2025-02-04 | criteria provided, single submitter | clinical testing | |
Molecular Genetics, |
RCV003993793 | SCV004812369 | benign | Metabolic myopathy | 2023-05-04 | criteria provided, single submitter | clinical testing | European Non-Finnish population allele frequency is 73.16%% (rs3071247, 161447/242952 alleles, 55293 homozygotes in gnomAD v2.1). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.1.0, this variant is classified as BENIGN. Following criteria are met: BA1 |
Diagnostic Laboratory, |
RCV000578107 | SCV000733726 | benign | Glycogen storage disease, type II | no assertion criteria provided | clinical testing | ||
Diagnostic Laboratory, |
RCV000578107 | SCV000733727 | benign | Glycogen storage disease, type II | no assertion criteria provided | clinical testing | ||
Mayo Clinic Laboratories, |
RCV000588321 | SCV000800867 | benign | not provided | 2015-12-07 | no assertion criteria provided | clinical testing | |
Natera, |
RCV000578107 | SCV001453597 | benign | Glycogen storage disease, type II | 2020-09-16 | no assertion criteria provided | clinical testing | |
Laboratory of Diagnostic Genome Analysis, |
RCV000588321 | SCV001800190 | likely benign | not provided | no assertion criteria provided | clinical testing | ||
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, |
RCV000078186 | SCV001958325 | benign | not specified | no assertion criteria provided | clinical testing | ||
Clinical Genetics DNA and cytogenetics Diagnostics Lab, |
RCV000588321 | SCV001964484 | likely benign | not provided | no assertion criteria provided | clinical testing |