F2RL1 p.Arg2=
c.4C>A · rs61749608 · VCV789180
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.01%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.042 | GERP -2.4, phastCons 0.2 |
| Overall | ||
| CADD | 8.05 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.01%
European (non-Finnish) · 11,826/1,172,778 alleles
Filtering AF
0.993%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.987%
Overall
0.845%
13,363/1,581,128 alleles · low-frequency
exomes 12,517/1,428,850 · genomes 846/152,278 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.01% | 99 |
| Remaining individualsnot grpmax-eligible | 0.959% | 104 |
| Admixed American | 0.603% | 166 |
| South Asian | 0.42% | 238 |
| Ashkenazi Jewishnot grpmax-eligible | 0.2% | 501 |
| African / African-American | 0.151% | 663 |
| Finnishnot grpmax-eligible | 0.131% | 762 |
| Middle Eastern | 0.105% | 952 |
| East Asian | 0.00227% | 44,090 |
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
- F2RL1
- Protein
- p.Arg2=
- Coding
- c.4C>A
- MANE Select
- NM_005242
- dbSNP
- rs61749608
- Type
- single nucleotide variant
- Location
- chr5:76819186 (GRCh38)
- Gene constraint
- LOEUF 0.989 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.92 · 7 PDB
Similar variants
- F2RL1 p.Arg2Gln Uncertain significance ★ ⚠ same residue
- F2RL1 p.Ala12Val Uncertain significance ★ ⚠ same type
- F2RL1 p.Ala188Thr Uncertain significance ★ ⚠ same type
- F2RL1 p.Ala18Ser Uncertain significance ★ ⚠ same type
- F2RL1 p.Ala220Val Uncertain significance ★ ⚠ same type
- F2RL1 p.Ala273Thr Uncertain significance ★ ⚠ same type
- F2RL1 p.Ala358Thr Uncertain significance ★ ⚠ same type
- F2RL1 p.Arg284Lys 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/f2rl1-p-arg2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown