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]

Variant: NM_000152.4(GAA):c.2780C>T (p.Thr927Ile)

Curation Version - 1.2
Curation History
JSON LD for Version 1.2

CA145778

92482 (ClinVar)

Gene: GAA

Condition: glycogen storage disease II

Inheritance Mode: Autosomal recessive inheritance

Link to MONDO

UUID: 0dace307-d73d-4361-89ee-42f551fed0d7

Approved on: 2020-01-23

Published on: 2020-05-19

HGVS expressions

NM_000152.4:c.2780C>T

NM_000152.4(GAA):c.2780C>T (p.Thr927Ile)

NC_000017.11:g.80118786C>T

CM000679.2:g.80118786C>T

NC_000017.10:g.78092585C>T

CM000679.1:g.78092585C>T

NC_000017.9:g.75707180C>T

NG_009822.1:g.22231C>T

NM_000152.3:c.2780C>T

NM_001079803.1:c.2780C>T

NM_001079804.1:c.2780C>T

NM_001079803.2:c.2780C>T

NM_001079804.2:c.2780C>T

NM_000152.5:c.2780C>T

NM_001079803.3:c.2780C>T

NM_001079804.3:c.2780C>T

ENST00000302262.7:c.2780C>T

ENST00000390015.7:c.2780C>T

ENST00000573556.1:n.733C>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 highest continental population minor allele frequency for c.2780C>T (p.Thr927Ile) in gnomAD v2.1.1 is 0.1317 in the African 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: 92482; 2 star review status) with six submitters classifying the variant as benign, and two as likely 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 0.1317 (African). 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.

Curation History

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