CMAS p.Lys26=
c.78G>A · rs138649790 · VCV778585
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.27%, 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 4 | GERP 0.92, phastCons 1 |
| Overall | ||
| CADD | 13.49 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.27%
African / African-American · 937/73,536 alleles
Filtering AF
1.21%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.18%
Overall
0.0682%
1,072/1,572,908 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.27% | 78 |
| Admixed American | 0.118% | 851 |
| Remaining individualsnot grpmax-eligible | 0.102% | 982 |
| Middle Eastern | 0.07% | 1,429 |
| South Asian | 0.00117% | 85,366 |
| European (non-Finnish) | 0.000431% | 232,135 |
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
- CMAS
- Protein
- p.Lys26=
- Coding
- c.78G>A
- MANE Select
- NM_018686
- dbSNP
- rs138649790
- Type
- single nucleotide variant
- Location
- chr12:22046381 (GRCh38)
- Gene constraint
- LOEUF 0.566 · pLI 0.83 (gnomAD)
- Structure
- AlphaFold pLDDT 88.10
- Residue 26
- the 'disordered' region
Similar variants
- CMAS p.Tyr403= Benign/Likely benign ★★ same type
- CMAS p.Ala328Pro Uncertain significance ★ ⚠ same type
- CMAS p.Arg175Cys Uncertain significance ★ ⚠ same type
- CMAS p.Arg175His Uncertain significance ★ ⚠ same type
- CMAS p.Arg18Leu Uncertain significance ★ ⚠ same type
- CMAS p.Arg203Cys Uncertain significance ★ ⚠ same type
- CMAS p.Arg241Gln Uncertain significance ★ ⚠ same type
- CMAS p.Arg415Gln 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/cmas-p-lys26 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown