ARMC5 p.Arg505=
c.1515C>T · rs115663676 · VCV785530
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.98%, afr)
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 0.82 | GERP -0.42, phastCons 0.3 |
| Overall | ||
| CADD | 6.603 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.98%
African / African-American · 2,222/74,584 alleles
Filtering AF
2.88%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.83%
Overall
0.155%
2,461/1,591,796 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.98% | 34 |
| Remaining individualsnot grpmax-eligible | 0.185% | 541 |
| Admixed American | 0.178% | 561 |
| Middle Eastern | 0.0501% | 1,997 |
| South Asian | 0.00337% | 29,713 |
| European (non-Finnish) | 0.00145% | 68,849 |
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.Arg505=
- Coding
- c.1515C>T
- MANE Select
- NM_001105247
- dbSNP
- rs115663676
- Type
- single nucleotide variant
- Location
- chr16:31464538 (GRCh38)
- Gene constraint
- LOEUF 0.772 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.27
- Residue 505
- the 'disordered' region; a UniProt-annotated variant site (in aimah2; uncertain significance); a UniProt-annotated variant site (in aimah2)
Similar variants
- ARMC5 p.Arg505Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- 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
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-arg505 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown