Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Link to SEPIO compliant JSON-LD document

Variant: NM_000152.5(GAA):c.2668G>C (p.Val890Leu)

CA8815831

255361 (ClinVar)

Gene: GAA

Condition: glycogen storage disease II

Inheritance Mode: Autosomal recessive inheritance

Link to MONDO

UUID: 0fe52acc-430a-4aaf-9a32-84fe84fbaa02

HGVS expressions

NM_000152.5:c.2668G>C

NM_000152.5(GAA):c.2668G>C (p.Val890Leu)

NC_000017.11:g.80118674G>C

CM000679.2:g.80118674G>C

NC_000017.10:g.78092473G>C

CM000679.1:g.78092473G>C

NC_000017.9:g.75707068G>C

NG_009822.1:g.22119G>C

ENST00000570803.6:c.2668G>C

ENST00000572080.2:c.*806G>C

ENST00000577106.6:c.2668G>C

ENST00000302262.8:c.2668G>C

ENST00000302262.7:c.2668G>C

ENST00000390015.7:c.2668G>C

ENST00000573556.1:n.621G>C

NM_000152.3:c.2668G>C

NM_001079803.1:c.2668G>C

NM_001079804.1:c.2668G>C

NM_000152.4:c.2668G>C

NM_001079803.2:c.2668G>C

NM_001079804.2:c.2668G>C

NM_001079803.3:c.2668G>C

NM_001079804.3:c.2668G>C

Benign

BA1

Evidence Links 0

Expert Panel

Lysosomal Diseases VCEP

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.2668G>C variant in GAA is predicted to result in the missense substitution of valine by leucine at amino acid position 890. The highest population minor allele frequency in gnomAD v2.1.1 is 0.02652 (812/30616 alleles with 13 homozygotes) in the South Asian population, which is higher than the ClinGen LSD VCEP’s threshold for BA1 (>0.01), and therefore meets this criterion (BA1). There is a ClinVar entry for this variant (Variation ID: 255361). In summary, this variant meets the criteria to be classified as benign for Pompe disease. GAA-specific ACMG/AMP criteria met, as specified by the ClinGen Lysosomal Diseases VCEP (Specifications Version 2.0): BA1. (Classified approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on October 1, 2023).

BA1

The highest population minor allele frequency in gnomAD v2.1.1 is 0.02652 (812/30616 alleles with 13 homozygotes) in the South Asian population, which is higher than the ClinGen LSD VCEP’s threshold for BA1 (>0.01), and therefore meets this criterion (BA1).

Approved on: 2023-10-01

Published on: 2024-03-26

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