Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_005249.5(FOXG1):c.237_239del (p.Pro80del)

CA961450348

1790283 (ClinVar)

Gene: FOXG1
Condition: FOXG1 disorder
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 9c57af25-ad68-4f80-964e-8da7827e1b38
Approved on: 2024-06-25
Published on: 2024-06-27

HGVS expressions

NM_005249.5:c.237_239del
NM_005249.5(FOXG1):c.237_239del (p.Pro80del)
NC_000014.9:g.28767516_28767518del
CM000676.2:g.28767516_28767518del
NC_000014.8:g.29236722_29236724del
CM000676.1:g.29236722_29236724del
NC_000014.7:g.28306473_28306475del
NG_009367.1:g.5436_5438del
ENST00000706482.1:c.237_239del
ENST00000313071.7:c.237_239del
ENST00000313071.6:c.237_239del
NM_005249.4:c.237_239del

Benign

Met criteria codes 2
BA1 BP3
Not Met criteria codes 1
PS4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Rett and Angelman-like Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for FOXG1 Version 3.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Rett and Angelman-like Disorders VCEP
The highest population minor allele frequency of the c.237_239del (p.Pro80del) variant in FOXG1 in gnomAD v4.1 is 0.00054 in the East Asian population, which is higher than the ClinGen Rett and Angelman-like Disorders VCEP threshold (≥0.0003) for BA1, and therefore meets this criterion (BA1). The p.Pro80del variant is an in-frame deletion present in a repetitive region of FOXG1 (BP3). In summary, the p.Pro80del variant in FOXG1 is classified as a benign variant based on the ACMG/AMP criteria (BA1, BP3).
Met criteria codes
BA1
The highest population minor allele frequency of the c.237_239del (p.Pro80del) variant in FOXG1 in gnomAD v4.1 is 0.00054 in the East Asian population, which is higher than the ClinGen Rett and Angelman-like Disorders VCEP threshold (≥0.0003) for BA1, and therefore meets this criterion (BA1).
BP3
The p.Pro80del variant is an in-frame deletion/duplication present in a repetitive region of FOXG1 (BP3).
Not Met criteria codes
PS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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