CBFA2T3 p.Pro84=
c.252G>A · rs539654957 · VCV2647018
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00813%, eas)
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 -16 | GERP -3.4 |
| Overall | ||
| CADD | 0.088 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00813%
East Asian · 3/36,878 alleles
Filtering AF
0.00636%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00596%
Overall
0.0069%
102/1,477,494 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00813% | 12,293 |
| European (non-Finnish) | 0.00778% | 12,850 |
| African / African-American | 0.00594% | 16,843 |
| Remaining individualsnot grpmax-eligible | 0.00526% | 19,015 |
| South Asian | 0.00417% | 23,980 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00384% | 26,014 |
| Finnishnot grpmax-eligible | 0.00172% | 58,272 |
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.Pro84=
- Coding
- c.252G>A
- MANE Select
- NM_005187
- dbSNP
- rs539654957
- Type
- single nucleotide variant
- Location
- chr16:88901556 (GRCh38)
- Gene constraint
- LOEUF 0.957 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.26 · 1 PDB
- Residue 84
- the 'mediates localization to the nucleus' region; the 'mediates interaction with pde7a (in isoform 2)' region; the 'required for nucleolar targeting (in isoform 1)' region; the 'disordered' region
Similar variants
- CBFA2T3 p.Pro84Leu Uncertain significance ★ ⚠ same residue
- CBFA2T3 p.Ala441Thr Likely benign ★★ same type
- CBFA2T3 p.Ala534= 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
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-pro84 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown