The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
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Variant: NM_000132.4(F8):c.5815G>C (p.Ala1939Pro)

CA414906836

811810 (ClinVar)

Gene: F8
Condition: hemophilia A
Inheritance Mode: X-linked inheritance
UUID: 3e57ff9f-e65d-4a65-952f-e8a8fdf65717
Approved on: 2024-10-11
Published on: 2024-10-11

HGVS expressions

NM_000132.4:c.5815G>C
NM_000132.4(F8):c.5815G>C (p.Ala1939Pro)
NC_000023.11:g.154904296C>G
CM000685.2:g.154904296C>G
NC_000023.10:g.154132571C>G
CM000685.1:g.154132571C>G
NC_000023.9:g.153785765C>G
NG_011403.1:g.123428G>C
NG_011403.2:g.123428G>C
ENST00000360256.9:c.5815G>C
ENST00000360256.8:c.5815G>C
NM_000132.3:c.5815G>C
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Uncertain Significance

Met criteria codes 3
PM2_Supporting PP4_Moderate PP3
Not Met criteria codes 1
PS4

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.5815G>C variant in F8 is a missense variant predicted to cause substitution of Alanine by Proline at amino acid 1939 in the last codon in exon 17, affecting the A3 domain of Factor VIII. It is reported affecting one individual in EAHAD with FVIII:C 1-stage =<1% with full gene sequencing and deletion/duplication analysis done, therefore it meets the phenotypic criteria for PP4_Moderate to be applied (PMID: 29296726). This variant has been reported in 1 proband with severe hemophilia A. However, PS4_Supporting cannot be applied because the individual also has a c.5493C>G i.e., p.(Thr1831Thr) variant (PMID: 30793713). The computational predictor REVEL gives a score of 0.908, which is above the threshold of 0.6, and Splice AI gives a score of 0.94 for donor loss, which is above the threshold of 0.5 set by the CFD VCEP and is evidence that correlates with impact to F8 function (PP3_Supporting). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). Due to conflicting evidence, this variant is classified as a variant of uncertain significance for Hemophilia A based on the ACMG/AMP criteria applied, as specified by the ClinGen Coagulation Factor Deficiency VCEP for F8 (version 1.0.0, released 10/5/2023): PP4_Moderate, PP3_Supporting, PM2_Supporting.
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting)
PP4_Moderate
The c.5815G>C is reported in one affected individual in supplemental table s7a-b and supplemental table 4a. Full gene sequencing and deletion/duplication analysis has been done. It is reported in EAHAD as FVIII:C 1-stage =<1%, therefore it meets the phenotypic criteria for PP4_Moderate to be applied. PMID: 29296726
PP3
It is highly conserved with a PhyloP 100 vertebrates score of 4.14 and PhastCons 100 vertebrates score of 1. The computational predictor REVEL gives a score of 0.908, which is above the threshold of 0.6, and Splice AI gives a score of 0.94 for donor loss, which is above the threshold of 0.5 set by the CFD VCEP and is evidence that correlates with impact to F8 function (PP3_Supporting).
Not Met criteria codes
PS4
This variant has been reported in 1 proband with severe hemophilia A. However, PS4_supporting cannot be applied because the individual also has a c.5493C>G i.e., p.(Thr1831Thr) variant (PMID: 30793713).
Curation History
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