ACTBL2 p.Cys18=
c.54C>T · rs141539012 · VCV730552
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.564%, 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 5.2 | GERP -0.98, phastCons 1 |
| Overall | ||
| CADD | 7.672 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.564%
African / African-American · 423/75,024 alleles
Filtering AF
0.519%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.502%
Overall
0.0293%
473/1,614,056 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.564% | 177 |
| Remaining individualsnot grpmax-eligible | 0.0464% | 2,155 |
| Middle Eastern | 0.033% | 3,031 |
| Admixed American | 0.0217% | 4,616 |
| East Asian | 0.00223% | 44,862 |
| European (non-Finnish) | 0.000424% | 236,002 |
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
- ACTBL2
- Protein
- p.Cys18=
- Coding
- c.54C>T
- MANE Select
- NM_001017992
- dbSNP
- rs141539012
- Type
- single nucleotide variant
- Location
- chr5:57482654 (GRCh38)
- Gene constraint
- LOEUF 1.624 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.97
Similar variants
- ACTBL2 p.Ala171Pro Uncertain significance ★ ⚠ same type
- ACTBL2 p.Ala171Ser Uncertain significance ★ ⚠ same type
- ACTBL2 p.Ala171Val Uncertain significance ★ same type
- ACTBL2 p.Ala27Asp Uncertain significance ★ ⚠ same type
- ACTBL2 p.Ala296Val Uncertain significance ★ ⚠ same type
- ACTBL2 p.Ala30Ser Uncertain significance ★ ⚠ same type
- ACTBL2 p.Ala322Thr Uncertain significance ★ ⚠ same type
- ACTBL2 p.Arg178Leu 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/actbl2-p-cys18 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown