Variant: NM_000152.5(GAA):c.1203G>A (p.Gln401=)

CA145749

92461 (ClinVar)

Gene: GAA

Condition: glycogen storage disease II

Inheritance Mode: Autosomal recessive inheritance

UUID: e6cd9da6-6885-4e33-8c81-2618a7acb9b5

HGVS expressions

NM_000152.5:c.1203G>A
NM_000152.5(GAA):c.1203G>A (p.Gln401=)
NC_000017.11:g.80108705G>A
CM000679.2:g.80108705G>A
NC_000017.10:g.78082504G>A
CM000679.1:g.78082504G>A
NC_000017.9:g.75697099G>A
NG_009822.1:g.12150G>A
NM_000152.3:c.1203G>A
NM_001079803.1:c.1203G>A
NM_001079804.1:c.1203G>A
NM_000152.4:c.1203G>A
NM_001079803.2:c.1203G>A
NM_001079804.2:c.1203G>A
NM_001079803.3:c.1203G>A
NM_001079804.3:c.1203G>A
ENST00000302262.7:c.1203G>A
ENST00000390015.7:c.1203G>A

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.1203G>A (p.Gln401=) in gnomAD v2.1.1 is 0.74003 in the European non-Finnish population. Note that the minor allele frequency is even higher in the Ashkenazi Jewish (0.77901) and European Finnish (0.76403) populations. These allele frequencies are higher than the ClinGen LSD VCEP’s BA1 threshold (>0.01), meeting this criterion. There is a ClinVar entry for this variant (Variation ID: 92461, two star review status), with 7 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.

Met criteria codes

• BA1: The highest continental population minor allele frequency in gnomAD v2.1.1 is 0.74003 (European non-Finnish). Note that the minor allele frequency is even higher in the Ashkenazi Jewish (0.77901) and European Finnish (0.76403) populations. These allele frequencies are higher than the ClinGen LSD VCEP’s BA1 threshold (>0.01), meeting this criterion.

Approved on: 2020-01-23

Published on: 2020-05-26