CMA1 p.Arg70=
c.210G>A · rs754716628 · VCV3146194
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0234%, amr)
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 -3.6 | GERP -4 |
| Overall | ||
| CADD | 7.736 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0234%
Admixed American · 14/59,932 alleles
Filtering AF
0.0141%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0112%
Overall
0.0013%
21/1,613,582 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0234% | 4,281 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,823 |
| Finnishnot grpmax-eligible | 0.00156% | 64,000 |
| African / African-American | 0.00134% | 74,840 |
| European (non-Finnish) | 0.00017% | 589,960 |
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
- CMA1
- Protein
- p.Arg70=
- Coding
- c.210G>A
- MANE Select
- NM_001836
- dbSNP
- rs754716628
- Type
- single nucleotide variant
- Location
- chr14:24506604 (GRCh38)
- Gene constraint
- LOEUF 1.578 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.55 · 42 PDB
- Residue 70
- a β-strand; the peptidase s1 domain
Similar variants
- CMA1 p.Gly46Arg Likely benign ★★ same type
- CMA1 p.Ala19Thr Uncertain significance ★ ⚠ same type
- CMA1 p.Ala246Thr Uncertain significance ★ ⚠ same type
- CMA1 p.Arg145Gln Uncertain significance ★ ⚠ same type
- CMA1 p.Arg151Gly Uncertain significance ★ ⚠ same type
- CMA1 p.Arg221Trp Uncertain significance ★ ⚠ same type
- CMA1 p.Asn45Lys Uncertain significance ★ ⚠ same type
- CMA1 p.Asn59Lys 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/cma1-p-arg70 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown