ARMC1 p.Ser4=
c.12C>T · rs146432746 · VCV2658630
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.256%, 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 -0.68 | phastCons 0.001 |
| Overall | ||
| CADD | 5.579 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.256%
Middle Eastern · 15/5,866 alleles
Filtering AF
0.158%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.127%
Overall
0.0154%
242/1,576,402 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.256% | 391 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0847% | 1,180 |
| Admixed American | 0.0515% | 1,943 |
| Remaining individualsnot grpmax-eligible | 0.0445% | 2,248 |
| African / African-American | 0.0299% | 3,343 |
| European (non-Finnish) | 0.0108% | 9,285 |
| South Asian | 0.00232% | 43,115 |
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
- ARMC1
- Protein
- p.Ser4=
- Coding
- c.12C>T
- MANE Select
- NM_018120
- dbSNP
- rs146432746
- Type
- single nucleotide variant
- Location
- chr8:65627387 (GRCh38)
- Gene constraint
- LOEUF 0.885 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.47
Similar variants
- ARMC1 p.Ser4Phe Uncertain significance ★ ⚠ same residue
- ARMC1 p.Ala25Val Uncertain significance ★ ⚠ same type
- ARMC1 p.Ala266Pro Uncertain significance ★ ⚠ same type
- ARMC1 p.Ala26Val Uncertain significance ★ ⚠ same type
- ARMC1 p.Ala273Thr Uncertain significance ★ ⚠ same type
- ARMC1 p.Arg127Cys Uncertain significance ★ ⚠ same type
- ARMC1 p.Arg127His Uncertain significance ★ ⚠ same type
- ARMC1 p.Arg141Ser 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/armc1-p-ser4 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown