F2R p.Val246=
c.738G>A · rs139693607 · VCV770163
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.04%, afr)
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 -0.46 | GERP -4.4, phastCons 0.012 |
| Overall | ||
| CADD | 2.803 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.04%
African / African-American · 782/75,040 alleles
Filtering AF
0.981%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.957%
Overall
0.053%
855/1,614,156 alleles · low-frequency
exomes 395/1,461,884 · genomes 460/152,272 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.04% | 96 |
| Admixed American | 0.0633% | 1,580 |
| Remaining individualsnot grpmax-eligible | 0.0432% | 2,315 |
| Middle Eastern | 0.033% | 3,031 |
| South Asian | 0.0022% | 45,538 |
| European (non-Finnish) | 0.000339% | 295,006 |
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.Val246=
- Coding
- c.738G>A
- MANE Select
- NM_001992
- dbSNP
- rs139693607
- Type
- single nucleotide variant
- Location
- chr5:76732963 (GRCh38)
- Gene constraint
- LOEUF 0.88 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.50 · 13 PDB
- Residue 246
- a β-strand
Similar variants
- F2R p.Leu38= Benign ★★ same type
- F2R p.Ser172= Benign ★★ same type
- F2R p.Tyr381Cys 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-val246 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown