ARMC12 p.Arg71=
c.213G>A · rs151133317 · VCV2656510
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.78%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.32 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.8 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 8.691 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.78%
Middle Eastern · 108/6,060 alleles
Filtering AF
1.51%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.41%
Overall
0.507%
8,188/1,614,060 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.78% | 56 |
| Admixed American | 0.651% | 154 |
| Ashkenazi Jewishnot grpmax-eligible | 0.611% | 164 |
| European (non-Finnish) | 0.565% | 177 |
| Remaining individualsnot grpmax-eligible | 0.458% | 219 |
| South Asian | 0.349% | 286 |
| Finnishnot grpmax-eligible | 0.293% | 342 |
| African / African-American | 0.0613% | 1,631 |
| East Asian | 0.0156% | 6,411 |
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
- ARMC12
- Protein
- p.Arg71=
- Coding
- c.213G>A
- MANE Select
- NM_001286574
- dbSNP
- rs151133317
- Type
- single nucleotide variant
- Location
- chr6:35738076 (GRCh38)
- Gene constraint
- LOEUF 0.88 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.08
- Residue 71
- the 'interaction with tbc1d15' region
Similar variants
- ARMC12 c.163+10C>T Uncertain significance ★ same type
- ARMC12 c.163+19G>C Uncertain significance ★ same type
- ARMC12 c.163+38G>C Uncertain significance ★ same type
- ARMC12 c.163+52C>G Uncertain significance ★ same type
- ARMC12 c.163+54G>A Uncertain significance ★ same type
- ARMC12 p.Ala104Val Uncertain significance ★ ⚠ same type
- ARMC12 p.Ala27Val Uncertain significance ★ ⚠ same type
- ARMC12 p.Ala37Ser 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/armc12-p-arg71 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown