CBFA2T3 p.Arg317=
c.951G>A · rs761363984 · VCV2647017
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0169%, amr)
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 1.4 | GERP -0.57, phastCons 1 |
| Overall | ||
| CADD | 11.62 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0169%
Admixed American · 10/59,126 alleles
Filtering AF
0.00912%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0069%
Overall
0.00269%
43/1,596,124 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0169% | 5,913 |
| European (non-Finnish) | 0.00257% | 38,963 |
| Finnishnot grpmax-eligible | 0.00162% | 61,600 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,664 |
| South Asian | 0.00111% | 90,124 |
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.Arg317=
- Coding
- c.951G>A
- MANE Select
- NM_005187
- dbSNP
- rs761363984
- Type
- single nucleotide variant
- Location
- chr16:88885212 (GRCh38)
- Gene constraint
- LOEUF 0.957 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.26 · 1 PDB
- Residue 317
- the 'mediates localization to the nucleus' region; the 'mediates interaction with pde7a (in isoform 2)' region; the 'disordered' region
Similar variants
- 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
- CBFA2T3 p.Ala460Pro 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-arg317 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown