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 label mismatch: F9 vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_000133.4(F9):c.769G>A (p.Val257Ile)

CA10529834

225354 (ClinVar)

Gene: F9
Condition: hemophilia B
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: 38622bb4-32e1-4c95-a640-f3cd85e5a081
Approved on: 2025-04-04
Published on: 2025-04-04

HGVS expressions

NM_000133.4:c.769G>A
NM_000133.4(F9):c.769G>A (p.Val257Ile)
NC_000023.11:g.139560786G>A
CM000685.2:g.139560786G>A
NC_000023.10:g.138642945G>A
CM000685.1:g.138642945G>A
NC_000023.9:g.138470611G>A
NG_007994.1:g.35051G>A
ENST00000218099.7:c.769G>A
ENST00000643157.1:n.1436G>A
ENST00000218099.6:c.769G>A
ENST00000394090.2:c.655G>A
NM_000133.3:c.769G>A
NM_001313913.1:c.655G>A
NM_001313913.2:c.655G>A
More

Benign

Met criteria codes 1
BA1
Not Met criteria codes 2
BP4 PP3

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.769G>A variant in F9 is a missense variant predicted to cause substitution of Valine by Isoleucine at amino acid 257 (p.Val257Ile). The highest population minor allele frequency in gnomAD v2.1.1 is 0.001548 (23/14862 alleles) in the East Asian population a grpmax FAF for exomes = 0.001015 and genomes = 0.0003535, which is higher than the ClinGen Coagulation Factor Deficiency VCEP threshold (>=0.0000556) for BA1, and therefore meets this criterion (BA1). In summary, this variant meets the criteria to be classified as Benign for Hemophilia B based on the ACMG/AMP criteria applied, as specified by the ClinGen Coagulation Factor Deficiency VCEP for F9 (version 1.0.0, released 10/5/2023): BA1.
Met criteria codes
BA1
The highest population minor allele frequency in gnomAD v2.1.1 is 0.001548 (23/14862 alleles) in the East Asian population with a grpmax FAF for exomes = 0.001015 and genomes= 0.0003535, which is higher than the ClinGen Coagulation Factor Deficiency VCEP threshold (>=0.0000556) for BA1, and therefore meets this criterion (BA1).
Not Met criteria codes
BP4
The computational predictor REVEL gives a score of 0.483, which is neither above nor below the thresholds predicting a damaging (>=0.6) or benign (<=0.3) impact on F9 function.
PP3
The computational predictor REVEL gives a score of 0.483, which is neither above nor below the thresholds predicting a damaging (>=0.6) or benign (<=0.3) impact on F9 function.
Curation History
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