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]

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Variant: NM_000152.5(GAA):c.921A>T (p.Ala307=)

CA145795

92490 (ClinVar)

Gene: GAA

Condition: glycogen storage disease II

Inheritance Mode: Autosomal recessive inheritance

Link to MONDO

UUID: caa7949e-c02b-4ceb-9886-4b8355f8e88b

Approved on: 2021-08-25

Published on: 2021-09-07

HGVS expressions

NM_000152.5:c.921A>T

NM_000152.5(GAA):c.921A>T (p.Ala307=)

ENST00000302262.8:c.921A>T

ENST00000302262.7:c.921A>T

ENST00000390015.7:c.921A>T

NM_000152.3:c.921A>T

NM_001079803.1:c.921A>T

NM_001079804.1:c.921A>T

NM_000152.4:c.921A>T

NM_001079803.2:c.921A>T

NM_001079804.2:c.921A>T

NM_001079803.3:c.921A>T

NM_001079804.3:c.921A>T

NC_000017.11:g.80107862A>T

CM000679.2:g.80107862A>T

NC_000017.10:g.78081661A>T

CM000679.1:g.78081661A>T

NC_000017.9:g.75696256A>T

NG_009822.1:g.11307A>T

Benign

BA1

Evidence Links 0

Expert Panel

Lysosomal Diseases VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Lysosomal Diseases VCEP

The NM_000152.5: c.921A>T (p.Ala307=) variant is a synonymous (silent) variant. The highest population minor allele frequency in gnomAD v2.1.1 is 0.23520 (569/24196 alleles, with 666 homozygotes) in the African 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: 92490; 2 star review status) with eight submitters classifying the variant as benign. In summary, this variant meets the criteria to be classified as benign for Pompe disease. ACMG/AMP criteria met, as specified by the ClinGen Lysosomal Storage Disorders Expert Panel (Specification Version 2.0): BA1. (Classification approved: August 17, 2021).

BA1

The highest population minor allele frequency in gnomAD v2.1.1 is 0.23520 (569/24196 alleles, with 666 homozygotes) in the African population, which is higher than the ClinGen LSD VCEP’s threshold for BA1 (>0.01), and therefore meets this criterion (BA1).

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