Variant: NM_000152.5(GAA):c.324T>C (p.Cys108=)

x This classification has been retracted/unpublished!

CA145781

92484 (ClinVar)

Gene: GAA

Condition: glycogen storage disease II

Inheritance Mode: Autosomal recessive inheritance

UUID: 1e551ab9-03f5-4129-9604-a9da6ebea09c

Approved on: 2020-01-23

Published on: 2020-05-26

HGVS expressions

NM_000152.5:c.324T>C
NM_000152.5(GAA):c.324T>C (p.Cys108=)
NC_000017.11:g.80104910T>C
CM000679.2:g.80104910T>C
NC_000017.10:g.78078709T>C
CM000679.1:g.78078709T>C
NC_000017.9:g.75693304T>C
NG_009822.1:g.8355T>C
ENST00000570803.6:c.324T>C
ENST00000572080.2:c.324T>C
ENST00000577106.6:c.324T>C
ENST00000302262.8:c.324T>C
ENST00000302262.7:c.324T>C
ENST00000390015.7:c.324T>C
ENST00000570803.5:c.324T>C
ENST00000577106.5:c.324T>C
NM_000152.3:c.324T>C
NM_001079803.1:c.324T>C
NM_001079804.1:c.324T>C
NM_000152.4:c.324T>C
NM_001079803.2:c.324T>C
NM_001079804.2:c.324T>C
NM_001079803.3:c.324T>C
NM_001079804.3:c.324T>C

Benign

• Met criteria codes: BA1

Expert Panel

Lysosomal Diseases VCEP

Criteria Specification Information

Evidence submitted by expert panel

Lysosomal Diseases VCEP

The highest continental population minor allele frequency for c.324T>C (p.Cys108=) in gnomAD (https://gnomad.broadinstitute.org/) is 0.8178 in the South Asian population. This is higher than the ClinGen LSD VCEP’s BA1 threshold (>0.01). Therefore, 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.

Met criteria codes

• BA1: The highest population minor allele frequency in gnomAD is 0.8178 (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.