ACTB p.Phe31=
c.93C>T · rs748892906 · VCV390871
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0121%, sas)
Conditions
1
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 0.36 | GERP -1.3, phastCons 0.96 |
| Overall | ||
| CADD | 13.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0121%
South Asian · 11/91,004 alleles
Filtering AF
0.00677%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00522%
Overall
0.0031%
50/1,611,686 alleles · ultra-rare
exomes 41/1,459,296 · genomes 9/152,390 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0121% | 8,273 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,190 |
| European (non-Finnish) | 0.00305% | 32,764 |
| Admixed American | 0.00167% | 59,972 |
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.Phe31=
- Coding
- c.93C>T
- MANE Select
- NM_001101
- dbSNP
- rs748892906
- Type
- single nucleotide variant
- Location
- chr7:5529565 (GRCh38)
- Gene constraint
- LOEUF 0.193 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 95.31 · 93 PDB
- Residue 31
- 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-phe31 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown