ARMC9 p.Arg87=
c.259C>A · rs372770167 · VCV2164836
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00975%, 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 2.8 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 5.161 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00975%
European (non-Finnish) · 115/1,180,022 alleles
Filtering AF
0.00826%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00774%
Overall
0.0075%
121/1,613,968 alleles · very rare
exomes 111/1,461,870 · genomes 10/152,098 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00975% | 10,261 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,620 |
| Finnishnot grpmax-eligible | 0.00156% | 64,022 |
| African / African-American | 0.00134% | 74,886 |
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.Arg87=
- Coding
- c.259C>A
- MANE Select
- NM_001352754
- dbSNP
- rs372770167
- Type
- single nucleotide variant
- Location
- chr2:231214912 (GRCh38)
- Gene constraint
- LOEUF 0.975 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.71
- Residue 87
- a UniProt-annotated variant site (in jbts30; uncertain significance)
Similar variants
- ARMC9 p.Arg87Ter Pathogenic/Likely pathogenic ★★ same residue
- ARMC9 p.Arg87Gln Conflicting classifications of pathogenicity ★ ⚠ 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.Arg299Ter Pathogenic/Likely pathogenic ★★ same type
- ARMC9 p.Arg343Cys Pathogenic/Likely pathogenic ★★ same type
- ARMC9 p.Thr293= Pathogenic/Likely pathogenic ★★ 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-arg87 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown