CBFA2T3 p.Ala534=
c.1602G>A · rs79678180 · VCV716461
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.15%, 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 0.075 | GERP -2, phastCons 0.73 |
| Overall | ||
| CADD | 11.41 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.15%
African / African-American · 3,111/75,036 alleles
Filtering AF
4.02%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.97%
Overall
0.222%
3,583/1,611,196 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.15% | 24 |
| Remaining individualsnot grpmax-eligible | 0.297% | 337 |
| Admixed American | 0.278% | 359 |
| Middle Eastern | 0.0331% | 3,025 |
| South Asian | 0.0132% | 7,586 |
| European (non-Finnish) | 0.00899% | 11,120 |
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
- CBFA2T3
- Protein
- p.Ala534=
- Coding
- c.1602G>A
- MANE Select
- NM_005187
- dbSNP
- rs79678180
- Type
- single nucleotide variant
- Location
- chr16:88879330 (GRCh38)
- Gene constraint
- LOEUF 0.957 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.26 · 1 PDB
- Residue 534
- a UniProt-annotated variant site (in a colorectal cancer sample; somatic mutation)
Similar variants
- CBFA2T3 p.Ala441Thr Likely benign ★★ same type
- CBFA2T3 p.Ala141Val Uncertain significance ★ ⚠ same type
- CBFA2T3 p.Ala272Thr Uncertain significance ★ ⚠ same type
- CBFA2T3 p.Ala350Thr Uncertain significance ★ ⚠ same type
- CBFA2T3 p.Ala449Thr Uncertain significance ★ ⚠ same type
- CBFA2T3 p.Ala451Thr Uncertain significance ★ ⚠ same type
- CBFA2T3 p.Ala460Pro Uncertain significance ★ ⚠ same type
- CBFA2T3 p.Ala460Thr 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/cbfa2t3-p-ala534 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown