ARMC5 p.Ala686=
c.2058G>A · rs11863886 · VCV3037824
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 18.1%, afr) — too common for a highly-penetrant pathogenic allele
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 -9 | GERP -3.1 |
| Overall | ||
| CADD | 0.287 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
18.1%
African / African-American · 13,537/74,888 alleles
Filtering AF
17.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 17.7%
Overall
2.19%
35,175/1,605,468 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 18.1% | 6 |
| South Asian | 17.6% | 6 |
| Amishnot grpmax-eligible | 14.1% | 7 |
| East Asian | 5.69% | 18 |
| Remaining individualsnot grpmax-eligible | 2.82% | 35 |
| Admixed American | 1.18% | 85 |
| Middle Eastern | 1.12% | 89 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0372% | 2,691 |
| European (non-Finnish) | 0.0356% | 2,809 |
| Finnishnot grpmax-eligible | 0.00179% | 55,932 |
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
- ARMC5
- Protein
- p.Ala686=
- Coding
- c.2058G>A
- MANE Select
- NM_001105247
- dbSNP
- rs11863886
- Type
- single nucleotide variant
- Location
- chr16:31466139 (GRCh38)
- Gene constraint
- LOEUF 0.772 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.27
- Residue 686
- a UniProt-annotated variant site (in aimah2; uncertain significance); a UniProt-annotated variant site (in aimah2)
Similar variants
- ARMC5 p.Arg173Ter Pathogenic ★★ same type
- ARMC5 p.Ala55Val Uncertain significance ★★ ⚠ same type
- ARMC5 p.Arg611Leu Uncertain significance ★★ ⚠ same type
- ARMC5 p.Arg690Gln Uncertain significance ★★ ⚠ same type
- ARMC5 p.Pro606Leu Uncertain significance ★★ ⚠ same type
- ARMC5 p.Ser266Thr Uncertain significance ★★ ⚠ same type
- ARMC5 p.Trp801Cys Uncertain significance ★★ ⚠ same type
- ARMC5 p.Ala110Thr Benign/Likely benign ★★ 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/armc5-p-ala686 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown