F5 p.Ser2172=
c.6516C>T · rs780625444 · VCV2884220
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.005%, nfe)
Conditions
2
Inborn genetic diseases
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 0.92 | GERP 0.79, phastCons 1 |
| Overall | ||
| CADD | 6.411 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
European (non-Finnish) · 59/1,179,556 alleles
Filtering AF
0.00394%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00361%
Overall
0.00384%
62/1,613,168 alleles · very rare
exomes 57/1,461,042 · genomes 5/152,126 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.005% | 19,992 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,813 |
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
- F5
- Protein
- p.Ser2172=
- Coding
- c.6516C>T
- MANE Select
- NM_000130
- dbSNP
- rs780625444
- Type
- single nucleotide variant
- Location
- chr1:169515456 (GRCh38)
- Gene constraint
- LOEUF 0.704 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.57 · 23 PDB
- Residue 2172
- a β-strand; the f5/8 type c 2 domain
Similar variants
- F5 c.1297-2A>G Pathogenic/Likely pathogenic ★★ same condition
- F5 p.Arg1030Ter Pathogenic ★★ same condition
- F5 p.Arg146Ter Pathogenic/Likely pathogenic ★★ same condition
- F5 p.Arg1621Ter Pathogenic/Likely pathogenic ★★ same condition
- F5 p.Arg1634Ter Pathogenic/Likely pathogenic ★★ same condition
- F5 p.Arg2102His Pathogenic/Likely pathogenic ★★ same condition
- F5 p.Arg740Ter Pathogenic/Likely pathogenic ★★ same condition
- F5 p.Asp96His 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/f5-p-ser2172 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown