ARMC2 p.Pro99=
c.297G>A · rs73524086 · VCV3033187
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.63%, afr)
Conditions
1
ARMC2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.26 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4 | GERP -5.1 |
| Overall | ||
| CADD | 4.828 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.63%
African / African-American · 1,212/74,542 alleles
Filtering AF
1.55%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.52%
Overall
0.0844%
1,358/1,608,220 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.63% | 62 |
| Admixed American | 0.124% | 806 |
| Remaining individualsnot grpmax-eligible | 0.0772% | 1,295 |
| South Asian | 0.00776% | 12,889 |
| European (non-Finnish) | 0.00161% | 62,016 |
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
- ARMC2
- Protein
- p.Pro99=
- Coding
- c.297G>A
- MANE Select
- NM_032131
- dbSNP
- rs73524086
- Type
- single nucleotide variant
- Location
- chr6:108868829 (GRCh38)
- Gene constraint
- LOEUF 0.936 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.57
- Residue 99
- the 'disordered' region
Disease context
ARMC2-related disorder
Similar variants
- ARMC2 p.Pro99Leu Uncertain significance ★ ⚠ same residue
- ARMC2 p.Ile185Val Conflicting classifications of pathogenicity ⚠ same condition
- ARMC2 c.219-4C>T Benign same condition
- ARMC2 p.Ala184Val Benign same condition
- ARMC2 p.Ala593= Benign same condition
- ARMC2 p.Gly438= Benign same condition
- ARMC2 p.Ile630Val Benign same condition
- ARMC2 p.Met166Thr Benign 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/armc2-p-pro99 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown