Variant: NM_000133.3(F9):c.108C>T (p.Asn36=)

CA10529735

367998 (ClinVar)

Gene: F9

Condition: hemophilia B

Inheritance Mode: X-linked inheritance

UUID: 427ba16e-f4c5-4c03-a24f-46db9355483b

Approved on: 2024-02-09

Published on: 2024-07-11

HGVS expressions

NM_000133.3:c.108C>T
NM_000133.3(F9):c.108C>T (p.Asn36=)
NC_000023.11:g.139537029C>T
CM000685.2:g.139537029C>T
NC_000023.10:g.138619188C>T
CM000685.1:g.138619188C>T
NC_000023.9:g.138446854C>T
NG_007994.1:g.11294C>T
ENST00000218099.7:c.108C>T
ENST00000218099.6:c.108C>T
ENST00000394090.2:c.108C>T
ENST00000479617.2:n.115C>T
NM_001313913.1:c.108C>T
NM_000133.4:c.108C>T
NM_001313913.2:c.108C>T

Benign

• Met criteria codes: BP7 BP4 BA1

Expert Panel

Coagulation Factor Deficiency VCEP

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

Evidence submitted by expert panel

Coagulation Factor Deficiency VCEP

The c.108C>T (p.Asn36=) variant is reported at an MAF of 0.0002820 (5/17730 alleles) in the South Asian population in gnomAD v2.1.1 with 1 hemizygote, meeting BA1 criteria of MAF > 0.0000556. SpliceAI predicts no splicing impact, with delta scores of 0, meeting BP4. The nucleotide is not conserved, with PhyloP score of -0.14 and PhastCons score of 0.031, meeting BP7. 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, BP4, BP7.

Met criteria codes

• BP7: SpliceAI predicts no splicing impact, with delta scores of 0. The nucleotide is not conserved, with PhyloP score of -0.14 and PhastCons score of 0.031
• BP4: SpliceAI predicts no splicing impact, with delta scores of 0.
• BA1: The c.108C>T (p.Asn36=) variant is reported at an MAF of 0.0002820 (5/17730 alleles) in the South Asian population in gnomAD v2.1.1 with 1 hemizygote, meeting BA1 criteria of MAF > 0.0000556.