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]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computer assertion could be determined for this classification!

Variant: NM_000133.4(F9):c.8G>A (p.Arg3His)

CA10529706

695909 (ClinVar)

Gene: F9
Condition: hemophilia B
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: 2053df3d-ec43-4e86-9818-57fac97974cb
Approved on: 2024-02-09
Published on: 2024-07-11

HGVS expressions

NM_000133.4:c.8G>A
NM_000133.4(F9):c.8G>A (p.Arg3His)
NC_000023.11:g.139530772G>A
CM000685.2:g.139530772G>A
NC_000023.10:g.138612931G>A
CM000685.1:g.138612931G>A
NC_000023.9:g.138440597G>A
NG_007994.1:g.5037G>A
ENST00000218099.7:c.8G>A
ENST00000218099.6:c.8G>A
ENST00000394090.2:c.8G>A
ENST00000479617.2:n.15G>A
NM_000133.3:c.8G>A
NM_001313913.1:c.8G>A
NM_001313913.2:c.8G>A
More

Benign

Met criteria codes 1
BA1
Not Met criteria codes 3
PP3 BP4 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 F9 Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Coagulation Factor Deficiency VCEP
The c.8G>A (p.Arg3His) variant is reported at an MAF of 0.001469 (28/19065 alleles) in the African/African American population in gnomAD v2.1.1 with 8 hemizygotes, meeting BA1 criteria of MAF > 0.0000556. gnomAD v3.1.1 reports 13 hemizygotes. REVEL score does not meet thresholds for PP3 or BP4. In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Coagulation Factor Deficiency Variant Curation Expert Panel for F9: BA1.
Met criteria codes
BA1
The c.8G>A (p.Arg3His) variant is reported at an MAF of 0.001469 (28/19065 alleles) in the African/African American population in gnomAD v2.1.1 with 8 hemizygotes, meeting BA1 criteria of MAF > 0.0000556. gnomAD v3.1.1 reports 13 hemizygotes.
Not Met criteria codes
PP3
The Arg3His missense variant has a REVEL score of 0.532 and does not meet the threshold for PP3 (>0.6)
BP4
The Arg3His missense variant has a REVEL score of 0.532 and does not meet the threshold for BP4 (<0.3). SpliceAI predicts no impact with delta scores of 0.
PS4
Proband from PMID: 1346077 does not meet F8 phenotype criteria due to presence of additional variant. Proband from internal data is not counted towards PS4 due to variant meeting BA1
Curation History
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