Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.21%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.26 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -12 | GERP -3.7 |
| Overall | ||
| CADD | 2.411 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.21%
African / African-American · 905/75,042 alleles
Filtering AF
1.14%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.11%
Overall
0.0626%
1,011/1,614,174 alleles · low-frequency
exomes 516/1,461,878 · genomes 495/152,296 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.21% | 83 |
| Remaining individualsnot grpmax-eligible | 0.0784% | 1,276 |
| Admixed American | 0.0616% | 1,622 |
| South Asian | 0.00329% | 30,362 |
| European (non-Finnish) | 0.00144% | 69,414 |
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
- STAT5A
- Protein
- p.Leu746=
- Coding
- c.2238C>T
- MANE Select
- NM_001288718
- dbSNP
- rs2230135
- Type
- single nucleotide variant
- Location
- chr17:42310522 (GRCh38)
- Gene constraint
- LOEUF 0.364 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 85.78 · 5 PDB
Similar variants
- STAT5A c.2063-4A>G Benign ★★ same type
- STAT5A p.Asp743= Benign ★★ same type
- STAT5A p.Val209Ala Benign ★★ same type
- STAT5A p.Ala213Val Uncertain significance ★ ⚠ same type
- STAT5A p.Ala318Thr Uncertain significance ★ ⚠ same type
- STAT5A p.Ala45Ser Uncertain significance ★ ⚠ same type
- STAT5A p.Ala510Thr Uncertain significance ★ ⚠ same type
- STAT5A p.Ala510Val 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/stat5a-p-leu746 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown