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_000133.3(F9):c.19A>T (p.Ile7Phe)

CA10529708

367997 (ClinVar)

Gene: F9
Condition: hemophilia B
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: b888a6e8-55cd-449a-a9d9-bc586edb7b6c
Approved on: 2024-02-09
Published on: 2024-07-11

HGVS expressions

NM_000133.3:c.19A>T
NM_000133.3(F9):c.19A>T (p.Ile7Phe)
NC_000023.11:g.139530783A>T
CM000685.2:g.139530783A>T
NC_000023.10:g.138612942A>T
CM000685.1:g.138612942A>T
NC_000023.9:g.138440608A>T
NG_007994.1:g.5048A>T
ENST00000218099.7:c.19A>T
ENST00000218099.6:c.19A>T
ENST00000394090.2:c.19A>T
ENST00000479617.2:n.26A>T
NM_001313913.1:c.19A>T
NM_000133.4:c.19A>T
NM_001313913.2:c.19A>T
More

Benign

Met criteria codes 2
BA1 BS2
Not Met criteria codes 2
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
NM_000133.3:c.19A>T variant results in a missense change in the signal peptide. This variant is reported at a frequency of 0.001643 (152/92537 alleles with 57 hemizygotes) in the non-Finnish European population in gnomAD v2.1.1, meeting the BA1 cut-off of >= 0.0000556. At least 2 individuals with the variant and normal FIX levels from the literature and internal laboratory data are reported (PMID: 29296726) meeting the BS2 criterion. In summary, the 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, BS2.
Met criteria codes
BA1
The Ile7Phe variant is reported at a frequency of 0.001643 (152/92537 alleles with 57 hemizygotes) in gnomAD v2.1.1 and at a frequency of 0.001600 (81/50618 alleles with 26 hemizygotes) in gnomAD v3, both in the non-Finnish European population, meeting the BA1 cut-off of >= 0.0000556 as determined by the CFD VCEP.
BS2
From internal laboratory data: Male individual with normal factor IX that was confirmed in follow-up testing as well. At least 2 individuals with the variant and normal FIX levels from PMID:29296726 and internal laboratory data meet criteria for BS2.
Not Met criteria codes
BP4
BP4 is not applied since neither CADD score of 17.04 nor REVEL score of 0.582 meet the threshold for BP4 determined by the CFD VCEP. (CADD: BP4 <11, PP3 <21; REVEL: BP4<0.3, PP3>0.6).
PS4
PS4 is not applied when BA1 is met. From internal laboratory data: the variant is reported in an individual with severe HB. PMID: 10094553 reports a patient with moderate HB.
Curation History
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