ACTB p.Leu105=
c.315G>C · rs139795454 · VCV1272674
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.048%, afr)
Conditions
2
Baraitser-Winter syndrome 1
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 0.016 | GERP -4.3, phastCons 0.75 |
| Overall | ||
| CADD | 9.041 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.048%
African / African-American · 36/75,054 alleles
Filtering AF
0.0356%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0313%
Overall
0.00285%
46/1,614,048 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.048% | 2,085 |
| Admixed American | 0.00833% | 12,004 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,251 |
| European (non-Finnish) | 0.000254% | 393,345 |
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
- ACTB
- Protein
- p.Leu105=
- Coding
- c.315G>C
- MANE Select
- NM_001101
- dbSNP
- rs139795454
- Type
- single nucleotide variant
- Location
- chr7:5529209 (GRCh38)
- Gene constraint
- LOEUF 0.193 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 95.31 · 93 PDB
- Residue 105
- a β-strand
Similar variants
- ACTB p.Ala22Thr Likely pathogenic ★★ same condition
- ACTB p.Ala7Thr Likely pathogenic ★★ same condition
- ACTB p.Arg147Cys Pathogenic ★★ same condition
- ACTB p.Arg183Trp Pathogenic ★★ same condition
- ACTB p.Arg196Cys Pathogenic ★★ same condition
- ACTB p.Arg196His Pathogenic ★★ same condition
- ACTB p.Arg196Leu Likely pathogenic ★★ same condition
- ACTB p.Arg206Gln Pathogenic/Likely pathogenic ★★ same condition
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/actb-p-leu105 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown