ARMC9 p.Pro703=
c.2109G>A · rs781559742 · VCV1346014
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0999%, mid)
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 -6.8 | GERP -1.8 |
| Overall | ||
| CADD | 0.11 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0999%
Middle Eastern · 6/6,008 alleles
Filtering AF
0.0434%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0296%
Overall
0.00475%
73/1,535,896 alleles · ultra-rare
exomes 64/1,383,676 · genomes 9/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0999% | 1,001 |
| European (non-Finnish) | 0.00523% | 19,114 |
| South Asian | 0.00357% | 28,017 |
| Remaining individualsnot grpmax-eligible | 0.00333% | 29,995 |
| Admixed American | 0.00196% | 50,972 |
| African / African-American | 0.00137% | 73,036 |
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.Pro703=
- Coding
- c.2109G>A
- MANE Select
- NM_001352754
- dbSNP
- rs781559742
- Type
- single nucleotide variant
- Location
- chr2:231355912 (GRCh38)
- Gene constraint
- LOEUF 0.975 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.71
- Residue 703
- the 'disordered' region
Similar variants
- ARMC9 p.Pro703fs Uncertain significance ★ 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.Arg87Ter 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-pro703 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown