ARMC9 p.Arg299=
c.897A>G · rs1223281820 · VCV2890961
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00667%, amr)
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 0.64 | GERP 0.005, phastCons 0.94 |
| Overall | ||
| CADD | 10.16 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00667%
Admixed American · 4/60,008 alleles
Filtering AF
0.00226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00135%
Overall
0.000248%
4/1,614,042 alleles · very rare
exomes 4/1,461,850 · genomes 0/152,192 · joint denominator
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
- ARMC9
- Protein
- p.Arg299=
- Coding
- c.897A>G
- MANE Select
- NM_001352754
- dbSNP
- rs1223281820
- Type
- single nucleotide variant
- Location
- chr2:231256603 (GRCh38)
- Gene constraint
- LOEUF 0.975 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.71
Similar variants
- ARMC9 p.Arg299Ter Pathogenic/Likely pathogenic ★★ same residue
- ARMC9 c.1773+1G>A Likely pathogenic ★★ same type
- ARMC9 c.178-1G>A Likely pathogenic ★★ same type
- ARMC9 c.178-2A>C Likely pathogenic ★★ same type
- ARMC9 p.Arg343Cys Pathogenic/Likely pathogenic ★★ same type
- ARMC9 p.Arg87Ter Pathogenic/Likely pathogenic ★★ same type
- ARMC9 p.Thr293= Pathogenic/Likely pathogenic ★★ same type
- ARMC9 p.Ala397Val 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/armc9-p-arg299 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown