F9 p.Asn36=
c.108C>T · rs184837275 · VCV367998
ClinGen expert panel — Coagulation Factor Deficiency VCEP
Benign for hemophilia B. Applied ACMG criteria (verbatim):
BP7 BP4 BA1
Curation rationale (ClinGen, verbatim)
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.
ClinGen Evidence Repository → · reported verbatim, not re-tallied by Sugi Variant.
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.67 | GERP 0.017, phastCons 1 |
| Overall | ||
| CADD | 5.735 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0695% | 1,439 |
| South Asian | 0.0234% | 4,269 |
| Remaining individualsnot grpmax-eligible | 0.0148% | 6,777 |
| European (non-Finnish) | 0.00616% | 16,231 |
| East Asian | 0.00298% | 33,612 |
| Admixed American | 0.0022% | 45,520 |
| Finnishnot grpmax-eligible | 0.00215% | 46,493 |
| African / African-American | 0.00175% | 57,181 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- F9
- Protein
- p.Asn36=
- Coding
- c.108C>T
- MANE Select
- NM_000133
- dbSNP
- rs184837275
- Type
- single nucleotide variant
- Location
- chrX:139537029 (GRCh38)
- Structure
- AlphaFold pLDDT 80.45 · 57 PDB
- Residue 36
- an α-helix
Disease context
hemophilia B — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: thrombophilia, X-linked, due to factor 9 defect
For Hemophilia B (Orphanet):
- Inheritance
- X-linked recessive
- Onset
- Childhood, Infancy, Neonatal
- Prevalence
- 1-9 / 100 000 (Europe)
Similar variants
- F9 p.Asn36Asp Likely benign ★ same residue
- F9 c.520+13A>G Pathogenic ★★★ same condition
- F9 c.88+1G>A Pathogenic ★★★ same condition
- F9 c.88+5G>T Likely pathogenic ★★★ same condition
- F9 p.Ala279Thr Pathogenic ★★★ ⚠ same condition
- F9 p.Ala337Pro Likely pathogenic ★★★ same condition
- F9 p.Ala337Thr Pathogenic ★★★ ⚠ same condition
- F9 p.Ala337Val Pathogenic ★★★ ⚠ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/f9-p-asn36 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown