17-80105137-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2_SupportingPVS1_Strong
This summary comes from the ClinGen Evidence Repository: The NM_000152.5:c.546+5G>T variant occurs in the donor splice region of intron 2 of GAA. RT-PCR of RNA from primary fibroblasts a patient who is compound heterozygous for c.[546+5G>T; 1726G>A] and c.1080C>G (p.Tyr360Ter) revealed a normal-sized fragment containing 2 sequences (one normal and one with a 3-bp insertion) and an aberrantly short fragment containing a deletion of exon 2 (PMID:34995642, Fig 6). Another study, using minigene analysis, showed that the variant results in almost complete skipping of exon 2 (PMID:31301153, Fig 3e, f). Consistent with this evidence, the computational predictor SpliceAI predicts loss of the donor splice site (score of 0.42) and gain of a splice donor 3bp downstream of the normal splice donor (score of 0.64). Any transcripts in which exon 2 is skipped would be missing the start codon and signal sequence (https://www.uniprot.org/uniprotkb/P10253/entry). This variant has been found in multiple individuals identified by newborn screening programs in Taiwan and Japan (PMID:20080426, 21232767, 31076647, 34995642). However, the variant always occurs in cis with pseudodeficiency variants (including c.1726G>A) which could be responsible for the reduced GAA activity observed in these individuals. One patient, who was compound heterozygous for the variant and c.1080C>G (p.Tyr360Ter), was reported to have initial CK elevation, and hypotonia for the first few years of life, but was later described as "normal" by the family at age 13 years (PMID:34995642). Therefore, despite the functional and predictive evidence indicating that this variant impacts splicing, the clinical significance of the variant is unclear. There has been no report of a patient with this variant who is clearly symptomatic for Pompe disease and, therefore, it is unknown if this variant may contribute to late-onset symptoms (neither PP4 nor PM3 were applied). The highest population minor allele frequency in gnomAD v2.1.1 is 0.0004978 in the East Asian population which is lower than ClinGen LD VCEP threshold of <0.001 (PM2_supporting). Other variants in the same donor splice site region have various classifications. For example, c.546+5G>A classified by the ClinGen LD VCEP as a variant of uncertain significance (ClinVar SCV004227903.1). Multiple other variants have been reported as pathogenic/likely pathogenic by ClinVar submitters (but not yet classified by the ClinGen LD VCEP) including c.546+2T>C, and c.546+2_+5del, and others in the same region have been classified in ClinVar as benign/Likely benign (not yet classified by the ClinGen LD VCEP) including c.546+4G>C; or VUS (c.546+3G>A). There is ClinVar entry for this variant (Variation ID: 557811). In summary, this variant has been classified as a variant of uncertain significance for Pompe disease by the ClinGen Lysosomal Disorders Variant Curation Expert Panel. Additional data, such as a report of a patient with clear symptoms of Pompe disease, or functional studies in muscle tissue, would be helpful. GAA-Specific ACMG-AMP criteria applied, as specified by the ClinGen LD VCEP (Specifications Version 2.0): PVS1_Strong, PM2_supporting.(Classification approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on November 5, 2024). LINK:https://erepo.genome.network/evrepo/ui/classification/CA8814901/MONDO:0009290/010
Frequency
Consequence
NM_000152.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| GAA | NM_000152.5 | c.546+5G>T | splice_region_variant, intron_variant | ENST00000302262.8 | NP_000143.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| GAA | ENST00000302262.8 | c.546+5G>T | splice_region_variant, intron_variant | 1 | NM_000152.5 | ENSP00000305692.3 |
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152246Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000382 AC: 9AN: 235344Hom.: 0 AF XY: 0.0000309 AC XY: 4AN XY: 129564
GnomAD4 exome AF: 0.00000828 AC: 12AN: 1450136Hom.: 0 Cov.: 36 AF XY: 0.00000833 AC XY: 6AN XY: 720654
GnomAD4 genome 0.00000657 AC: 1AN: 152246Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74384
ClinVar
Submissions by phenotype
Glycogen storage disease, type II Pathogenic:6Uncertain:3
| Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Dec 30, 2022 | Variant summary: GAA c.546+5G>T alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Three predict the variant abolishes the canonical 5' splicing donor site. One predicts the variant weakens the canonical 5' splicing donor site. At least one publication reports experimental evidence that this variant affects mRNA splicing resulting in skipping of exon 2 (Goina_2019). The variant allele was found at a frequency of 3.8e-05 in 235344 control chromosomes. c.546+5G>T has been reported in the literature as a homozygous or compound heterozygous genotype in newborns affected with later onset Glycogen Storage Disease, Type 2 (Pompe Disease) (example, Chien_2011). These data indicate that the variant may be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function (Chien_2011). The most pronounced variant effect results in <10% of normal alpha glucosidase activity in lymphocytes and fibroblasts from a homozygous individual. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments (P/LP, n=3; VUS, n=2). Based on the evidence outlined above, the variant was classified as pathogenic. - |
| Likely pathogenic, no assertion criteria provided | clinical testing | Natera, Inc. | Oct 20, 2020 | - - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 09, 2024 | - - |
| Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Apr 06, 2018 | - - |
| Uncertain significance, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 22, 2021 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Feb 21, 2024 | - - |
| Likely pathogenic, criteria provided, single submitter | curation | Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard | Jan 22, 2020 | The c.546+5G>T variant in GAA has been reported in at least two Taiwanese individuals with glycogen storage disease (PMID: 20080426, 21232767), and has been identified in 0.050% (9/18078) of East Asian chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs756024023). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. This variant has also been reported in ClinVar as a VUS by Counsyl (VariationID: 557811). This variant is located in the 5' splice region. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. The phenotype of individuals homozygous and compound heterozygous for this variant is highly specific for glycogen storage disease based on enzyme activity in in lymphocytes and fibroblasts being <10% of controls, consistent with disease (PMID: 21232767). Additionally, the presence of this variant in combination with a reported likely pathogenic variant p.Tyr360Ter, as well as a homozygous occurrence (PMID: 21232767), in individuals with glycogen storage disease increases the likelihood that the c.546+5G>T variant is pathogenic. In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic. ACMG/AMP Criteria applied: PM3, PM2, PP4_moderate, PP3 (Richards 2015). - |
| Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 09, 2023 | This sequence change falls in intron 2 of the GAA gene. It does not directly change the encoded amino acid sequence of the GAA protein. RNA analysis indicates that this variant induces altered splicing and is likely to result in the loss of the initiator methionine. This variant is present in population databases (rs756024023, gnomAD 0.05%). This variant has been observed in individual(s) with Pompe disease (PMID: 21232767). ClinVar contains an entry for this variant (Variation ID: 557811). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 2, and is expected to result in the loss of the initiator methionine (PMID: 31301153). This variant disrupts the p.Arg190 amino acid residue in GAA. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 21484825, 23000108, 24444888, 29149851, 31076647). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. - |
| Uncertain significance, reviewed by expert panel | curation | ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel | Nov 05, 2024 | The NM_000152.5:c.546+5G>T variant occurs in the donor splice region of intron 2 of GAA. RT-PCR of RNA from primary fibroblasts a patient who is compound heterozygous for c.[546+5G>T; 1726G>A] and c.1080C>G (p.Tyr360Ter) revealed a normal-sized fragment containing 2 sequences (one normal and one with a 3-bp insertion) and an aberrantly short fragment containing a deletion of exon 2 (PMID: 34995642, Fig 6). Another study, using minigene analysis, showed that the variant results in almost complete skipping of exon 2 (PMID: 31301153, Fig 3e, f). Consistent with this evidence, the computational predictor SpliceAI predicts loss of the donor splice site (score of 0.42) and gain of a splice donor 3bp downstream of the normal splice donor (score of 0.64). Any transcripts in which exon 2 is skipped would be missing the start codon and signal sequence (https://www.uniprot.org/uniprotkb/P10253/entry). This variant has been found in multiple individuals identified by newborn screening programs in Taiwan and Japan (PMID: 20080426, 21232767, 31076647, 34995642). However, the variant always occurs in cis with pseudodeficiency variants (including c.1726G>A) which could be responsible for the reduced GAA activity observed in these individuals. One patient, who was compound heterozygous for the variant and c.1080C>G (p.Tyr360Ter), was reported to have initial CK elevation, and hypotonia for the first few years of life, but was later described as "normal" by the family at age 13 years (PMID: 34995642). Therefore, despite the functional and predictive evidence indicating that this variant impacts splicing, the clinical significance of the variant is unclear. There has been no report of a patient with this variant who is clearly symptomatic for Pompe disease and, therefore, it is unknown if this variant may contribute to late-onset symptoms (neither PP4 nor PM3 were applied). The highest population minor allele frequency in gnomAD v2.1.1 is 0.0004978 in the East Asian population which is lower than ClinGen LD VCEP threshold of <0.001 (PM2_supporting). Other variants in the same donor splice site region have various classifications. For example, c.546+5G>A classified by the ClinGen LD VCEP as a variant of uncertain significance (ClinVar SCV004227903.1). Multiple other variants have been reported as pathogenic/likely pathogenic by ClinVar submitters (but not yet classified by the ClinGen LD VCEP) including c.546+2T>C, and c.546+2_+5del, and others in the same region have been classified in ClinVar as benign/Likely benign (not yet classified by the ClinGen LD VCEP) including c.546+4G>C; or VUS (c.546+3G>A). There is ClinVar entry for this variant (Variation ID: 557811). In summary, this variant has been classified as a variant of uncertain significance for Pompe disease by the ClinGen Lysosomal Disorders Variant Curation Expert Panel. Additional data, such as a report of a patient with clear symptoms of Pompe disease, or functional studies in muscle tissue, would be helpful. GAA-Specific ACMG-AMP criteria applied, as specified by the ClinGen LD VCEP (Specifications Version 2.0): PVS1_Strong, PM2_supporting. (Classification approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on November 5, 2024). - |
not provided Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Oct 20, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at