ARMC9 p.Ser508=
c.1524G>A · rs767400789 · VCV1947188
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.33 | acceptor loss · deltas |
|---|---|---|
| Pangolin | Δ0.32 | loss · gain 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -5 | GERP -2.8 |
| Overall | ||
| CADD | 4.021 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
East Asian · 6/44,898 alleles
Filtering AF
0.00579%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00394%
Overall
0.00273%
44/1,613,934 alleles · ultra-rare
exomes 42/1,461,780 · genomes 2/152,154 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0134% | 7,483 |
| South Asian | 0.00549% | 18,214 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,240 |
| European (non-Finnish) | 0.00254% | 39,334 |
| Finnishnot grpmax-eligible | 0.00156% | 64,022 |
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.Ser508=
- Coding
- c.1524G>A
- MANE Select
- NM_001352754
- dbSNP
- rs767400789
- Type
- single nucleotide variant
- Location
- chr2:231278431 (GRCh38)
- Gene constraint
- LOEUF 0.975 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.71
Similar variants
- 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
- 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-ser508 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown