Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.43%, afr)
Conditions
1
factor VII deficiency
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 0.13 | GERP -0.45, phastCons 0.001 |
| Overall | ||
| CADD | 3.364 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.43%
African / African-American · 2,566/74,864 alleles
Filtering AF
3.32%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.27%
Overall
0.197%
3,161/1,606,486 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.43% | 29 |
| Admixed American | 0.327% | 306 |
| Remaining individualsnot grpmax-eligible | 0.243% | 411 |
| Middle Eastern | 0.231% | 432 |
| European (non-Finnish) | 0.0188% | 5,325 |
| South Asian | 0.0144% | 6,922 |
| East Asian | 0.00447% | 22,360 |
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
- F7
- Protein
- p.Pro36=
- Coding
- c.108G>A
- MANE Select
- NM_019616 · reported on NM_000131
- dbSNP
- rs3093238
- Type
- single nucleotide variant
- Location
- chr13:113106888 (GRCh38)
- Gene constraint
- LOEUF 1.113 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 82.64 · 114 PDB
Similar variants
- F7 p.Pro36Leu Likely benign ★ same residue
- F7 c.364+1G>A Pathogenic/Likely pathogenic ★★ same condition
- F7 c.615+1G>T Pathogenic/Likely pathogenic ★★ same condition
- F7 c.-30A>C Likely pathogenic ★★ same condition
- F7 c.-55C>T Pathogenic/Likely pathogenic ★★ same condition
- F7 c.-61T>G Likely pathogenic ★★ same condition
- F7 p.Ala282Val Pathogenic/Likely pathogenic ★★ ⚠ same condition
- F7 p.Ala332Val Pathogenic/Likely 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/f7-p-pro36 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown