Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.647%, nfe)
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 -9.6 | GERP -4.5 |
| Overall | ||
| CADD | 0.245 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.647%
European (non-Finnish) · 7,634/1,180,046 alleles
Filtering AF
0.635%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.63%
Overall
0.52%
8,402/1,614,234 alleles · rare
exomes 7,880/1,461,892 · genomes 522/152,342 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.647% | 155 |
| Remaining individualsnot grpmax-eligible | 0.418% | 240 |
| Finnishnot grpmax-eligible | 0.398% | 251 |
| Middle Eastern | 0.148% | 674 |
| Admixed American | 0.117% | 857 |
| African / African-American | 0.113% | 883 |
| South Asian | 0.0955% | 1,047 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
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
- F2R
- Protein
- p.Ser172=
- Coding
- c.516T>G
- MANE Select
- NM_001992
- dbSNP
- rs5894
- Type
- single nucleotide variant
- Location
- chr5:76732741 (GRCh38)
- Gene constraint
- LOEUF 0.88 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.50 · 13 PDB
- Residue 172
- an α-helix
Similar variants
- F2R p.Leu38= Benign ★★ same type
- F2R p.Tyr381Cys Benign ★★ same type
- F2R p.Val246= Benign ★★ same type
- F2R p.Ala10Val Uncertain significance ★ ⚠ same type
- F2R p.Ala203Thr Uncertain significance ★ ⚠ same type
- F2R p.Ala268Ser Uncertain significance ★ ⚠ same type
- F2R p.Arg214Ser Uncertain significance ★ ⚠ same type
- F2R p.Arg5Trp Uncertain significance ★ ⚠ same type
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/f2r-p-ser172 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown