The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

  • See Evidence submitted by expert panel for details.

Variant: NM_000152.5(GAA):c.858+7_858+8insAGCGGGC

CA145794

92489 (ClinVar)

Gene: GAA
Condition: glycogen storage disease II
Inheritance Mode: Autosomal recessive inheritance
UUID: ea364aeb-ae6b-4709-a498-251ba65289a1
Approved on: 2020-05-19
Published on: 2020-06-02

HGVS expressions

NM_000152.5:c.858+7_858+8insAGCGGGC
NM_000152.5(GAA):c.858+7_858+8insAGCGGGC
NM_000152.3:c.858+7_858+8insAGCGGGC
NM_001079803.1:c.858+7_858+8insAGCGGGC
NM_001079804.1:c.858+7_858+8insAGCGGGC
NM_000152.4:c.858+7_858+8insAGCGGGC
NM_001079803.2:c.858+7_858+8insAGCGGGC
NM_001079804.2:c.858+7_858+8insAGCGGGC
NM_001079803.3:c.858+7_858+8insAGCGGGC
NM_001079804.3:c.858+7_858+8insAGCGGGC
ENST00000302262.7:c.858+7_858+8insAGCGGGC
ENST00000390015.7:c.858+7_858+8insAGCGGGC
NC_000017.11:g.80107729_80107730insAGCGGGC
CM000679.2:g.80107729_80107730insAGCGGGC
NC_000017.10:g.78081528_78081529insAGCGGGC
CM000679.1:g.78081528_78081529insAGCGGGC
NC_000017.9:g.75696123_75696124insAGCGGGC
NG_009822.1:g.11174_11175insAGCGGGC
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Benign

Met criteria codes 1
BA1

Evidence Links 0

Expert Panel

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.858+7_858+8insAGCGGGC in gnomAD v.2.1.1 is 0.7353 in the European non-Finnish population. This allele frequency is higher than the ClinGen LSD VCEP’s BA1 threshold (>0.01), meeting this criterion. Note that the minor allele frequency is even higher in the Ashkenazi Jewish (0.7783) and European Finnish (0.7613) populations. There is a ClinVar entry for this variant (Variation ID: 92489, 2 star review status), with 10 submitters all 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 0.7353 in the European (non-Finnish) population, which is higher than the ClinGen LSD VCEP threshold (>0.01) for BA1, and therefore meets this criterion. Of note, the minor allele frequency is even higher is Ashkenazi Jewish (0.7783) and European Finnish (0.7613).
Curation History
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