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_000152.4(GAA):c.2338G>A (p.Val780Ile)

CA145769

92476 (ClinVar)

Gene: GAA

Condition: glycogen storage disease II

Inheritance Mode: Autosomal recessive inheritance

Link to MONDO

UUID: 69ccf2de-d1f6-4cf9-b273-379884a992c0

HGVS expressions

NM_000152.4:c.2338G>A

NM_000152.4(GAA):c.2338G>A (p.Val780Ile)

NC_000017.11:g.80117606G>A

CM000679.2:g.80117606G>A

NC_000017.10:g.78091405G>A

CM000679.1:g.78091405G>A

NC_000017.9:g.75706000G>A

NG_009822.1:g.21051G>A

NM_000152.3:c.2338G>A

NM_001079803.1:c.2338G>A

NM_001079804.1:c.2338G>A

NM_001079803.2:c.2338G>A

NM_001079804.2:c.2338G>A

NM_000152.5:c.2338G>A

NM_001079803.3:c.2338G>A

NM_001079804.3:c.2338G>A

ENST00000302262.7:c.2338G>A

ENST00000390015.7:c.2338G>A

ENST00000573556.1:n.291G>A

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 highest continental population minor allele frequency for c.2338G>A (p.Val780Ile) in gnomAD v2.1.1 is 0.8129 in the South Asian population. This is higher than the ClinGen LSD VCEP’s BA1 threshold (>0.01), therefore meeting the BA1 criterion. There is a ClinVar entry for this variant (Variation ID: 92476; 2 star review status) with six submitters 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.

BA1

The highest population minor allele frequency in gnomAD is 0.8129 (South Asian). This is higher than the ClinGen LSD VCEP threshold (>0.01) for BA1. Therefore, the allele frequency data for this variant meet the BA1 criterion.

Approved on: 2020-01-23

Published on: 2020-05-19

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