Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_000152.5(GAA):c.2400C>T (p.Ser800=)

CA180077

167115 (ClinVar)

Gene: GAA
Condition: glycogen storage disease II
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: f1b0a8d8-3cc5-4dc5-9a2a-21e4715f92e1
Approved on: 2024-08-06
Published on: 2024-09-03

HGVS expressions

NM_000152.5:c.2400C>T
NM_000152.5(GAA):c.2400C>T (p.Ser800=)
NC_000017.11:g.80117668C>T
CM000679.2:g.80117668C>T
NC_000017.10:g.78091467C>T
CM000679.1:g.78091467C>T
NC_000017.9:g.75706062C>T
NG_009822.1:g.21113C>T
ENST00000570803.6:c.2400C>T
ENST00000572080.2:c.*538C>T
ENST00000577106.6:c.2400C>T
ENST00000302262.8:c.2400C>T
ENST00000302262.7:c.2400C>T
ENST00000390015.7:c.2400C>T
ENST00000573556.1:n.353C>T
NM_000152.3:c.2400C>T
NM_001079803.1:c.2400C>T
NM_001079804.1:c.2400C>T
NM_000152.4:c.2400C>T
NM_001079803.2:c.2400C>T
NM_001079804.2:c.2400C>T
NM_001079803.3:c.2400C>T
NM_001079804.3:c.2400C>T

Benign

Met criteria codes 1
BA1
Not Met criteria codes 1
PM2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Lysosomal Storage Disorders Variant Curation Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 2

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Lysosomal Diseases VCEP
The NM_000152.5:c.2400C>T variant in GAA is a synonymous (silent) variant (p.Ser800=) that is not predicted to impact splicing. The highest population minor allele frequency in gnomAD v2.1.1. is 0.02504 (617/24640 alleles; 9 homozygotes) in the African/African American population, which is higher than the ClinGen Lysosomal Diseases VCEP’s threshold for BA1 (>0.01), and therefore meets this criterion (BA1). There is a ClinVar entry for this variant (Variation ID: 167115. 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 Lysosomal Diseases Variant Curation Expert Panel (specifications Version 2.0): BA1. (Classification approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on August 6, 2024).
Met criteria codes
BA1
The highest population minor allele frequency in gnomAD v2.1.1. is 0.02504 (617/24640 alleles; 9 homozygotes) in the African/African American population, which is higher than the ClinGen Lysosomal Diseases VCEP’s threshold for BA1 (>0.01), and therefore meets this criterion (BA1).
Not Met criteria codes
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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