ARMC5 p.Ser98=
c.294G>T · rs372292806 · VCV715819
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.173%, 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 -0.62 | GERP -3.8 |
| Overall | ||
| CADD | 1.093 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.173%
European (non-Finnish) · 2,001/1,154,154 alleles
Filtering AF
0.167%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.164%
Overall
0.134%
2,071/1,548,976 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.173% | 577 |
| Remaining individualsnot grpmax-eligible | 0.0714% | 1,401 |
| African / African-American | 0.0328% | 3,044 |
| East Asian | 0.00242% | 41,380 |
| Finnishnot grpmax-eligible | 0.00209% | 47,788 |
| Admixed American | 0.00193% | 51,844 |
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.Ser98=
- Coding
- c.294G>T
- MANE Select
- NM_001105247
- dbSNP
- rs372292806
- Type
- single nucleotide variant
- Location
- chr16:31459818 (GRCh38)
- Gene constraint
- LOEUF 0.772 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.27
- Residue 98
- a UniProt-annotated variant site (in aimah2; uncertain significance); a UniProt-annotated variant site (in aimah2); the 'disordered' region
Similar variants
- ARMC5 p.Ser98Pro Uncertain significance ★ ⚠ same residue
- ARMC5 p.Ser98Thr Uncertain significance ★ ⚠ 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
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-ser98 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown