ADGRF3 p.Arg498=
c.1494G>A · rs149862488 · VCV2650744
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0291%, 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 -0.099 | GERP -5.5 |
| Overall | ||
| CADD | 2.184 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0291%
European (non-Finnish) · 343/1,179,874 alleles
Filtering AF
0.0265%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0255%
Overall
0.0226%
364/1,612,628 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0291% | 3,440 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,242 |
| Admixed American | 0.00667% | 14,999 |
| African / African-American | 0.00401% | 24,966 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,602 |
| South Asian | 0.0033% | 30,348 |
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
- ADGRF3
- Protein
- p.Arg498=
- Coding
- c.1494G>A
- MANE Select
- NM_001321971
- dbSNP
- rs149862488
- Type
- single nucleotide variant
- Location
- chr2:26312030 (GRCh38)
- Gene constraint
- LOEUF 1.069 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.07
Similar variants
- ADGRF3 p.Arg498Ser Likely benign ★ same residue
- ADGRF3 c.115-1315G>A Uncertain significance ★ ⚠ same type
- ADGRF3 c.115-1349C>A Uncertain significance ★ ⚠ same type
- ADGRF3 c.115-1360G>A Uncertain significance ★ ⚠ same type
- ADGRF3 c.115-1415G>A Uncertain significance ★ ⚠ same type
- ADGRF3 c.115-1448A>G Uncertain significance ★ ⚠ same type
- ADGRF3 c.115-1453C>T Uncertain significance ★ ⚠ same type
- ADGRF3 c.115-1477C>T 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/adgrf3-p-arg498 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown