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_000132.3(F8):c.2215G>A (p.Glu739Lys)

CA255139

10247 (ClinVar)

Gene: F8
Condition: hemophilia A
Inheritance Mode: X-linked inheritance
UUID: 70229bdd-5bf3-4644-8ab6-49706b300e62
Approved on: 2024-02-02
Published on: 2024-07-11

HGVS expressions

NM_000132.3:c.2215G>A
NM_000132.3(F8):c.2215G>A (p.Glu739Lys)
NC_000023.11:g.154931575C>T
CM000685.2:g.154931575C>T
NC_000023.10:g.154159850C>T
CM000685.1:g.154159850C>T
NC_000023.9:g.153813044C>T
NG_011403.1:g.96149G>A
NG_011403.2:g.96149G>A
ENST00000360256.9:c.2215G>A
ENST00000647125.1:c.*1881G>A
ENST00000360256.8:c.2215G>A
NM_000132.4:c.2215G>A

Pathogenic

Met criteria codes 6
PS4 PS3 PP3 PP4_Moderate PP1_Moderate PM2_Supporting

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Coagulation Factor Deficiency Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for F8 Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Coagulation Factor Deficiency VCEP
The c.2215G>A (p.Glu739Lys) missense variant is absent from males in both gnomAD v2.1.1 and v3.1.1, meeting the PM2_Supporting criteria. The variant has a REVEL score of 0.614 (>0.6), meeting PP3 criteria. At least 13 patients with mild hemophilia A are reported in the literature and internal laboratory data meeting F8 phenotype criteria (PMID: 24452774, 23711237, 21166991, 8547094, 16972227), which meets the PS4_Very strong and PP4_Moderate criteria. This variant has been labeled as an inverse discrepant variant, where the one-stage assays show lower factor VIII levels than the two-stage, or chromogenic, assays (EAHAD database; PMID: 32232366). There were multiple related individuals across 6 different families reported that were genotyped, but their specific relation was not stated, so the PP1 was capped at the moderate weight to be conservative (PMID: 24452774). In-vitro assays in COS-1 cells show FVIII-Glu739Lys results in lower FVIII:C in the mild range, as observed in patients with this variant and hemophilia A (PMID: 30997536). In summary, this variant meets criteria to be classified as pathogenic. ACMG/AMP criteria applied, as specified by the Coagulation Factor Deficiency Variant Curation Expert Panel for F8: PS4_Very strong, PS3, PP1_Moderate, PP4_Moderate, PP3, PM2_Supporting.
Met criteria codes
PS4
At least 13 patients with mild hemophilia A are reported in the literature and internal laboratory data meeting F8 phenotype criteria (PMID: 24452774, 23711237, 21166991, 8547094, 16972227, 29296726), which meets the PS4_Very strong code.
PS3
In-vitro assays in COS-1 cells show FVIII-Glu739Lys results in lower FVIII:C in the mild range, as observed in patients with this variant and hemophilia A (PMID: 30997536).
PP3
The c.2215G>A (p.Glu739Lys) missense variant has a REVEL score of 0.614 (>0.6), meeting PP3 criteria
PP4_Moderate
One individual with mild hemophilia A with factor VIII activity level of 32%. Participant had full F8 and F9 gene deletion and duplication analysis through MLOF study.
PP1_Moderate
Variant was identified in 13 individuals from 6 families. The relationships in these 6 families were not provided, so we assumed a minimal number of 7 meioses and applying at only the PP1_Moderate level to be conservative.
PM2_Supporting
The variant is absent from males in gnomAD.
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