TET3 p.Val293=
c.879G>A · rs375792236 · VCV3024667
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0992%, nfe)
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 7.5 | GERP 1.5, phastCons 1 |
| Overall | ||
| CADD | 9.513 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0992%
European (non-Finnish) · 1,171/1,179,876 alleles
Filtering AF
0.0945%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0926%
Overall
0.075%
1,210/1,613,308 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0992% | 1,008 |
| Remaining individualsnot grpmax-eligible | 0.04% | 2,499 |
| Middle Eastern | 0.0164% | 6,084 |
| African / African-American | 0.0133% | 7,491 |
| Finnishnot grpmax-eligible | 0.00315% | 31,737 |
| Admixed American | 0.00167% | 60,006 |
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
- TET3
- Protein
- p.Val293=
- Coding
- c.879G>A
- MANE Select
- NM_001287491
- dbSNP
- rs375792236
- Type
- single nucleotide variant
- Location
- chr2:74046796 (GRCh38)
- Gene constraint
- LOEUF 0.213 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 52.49 · 2 PDB
Similar variants
- TET3 p.Arg1034Ter Pathogenic/Likely pathogenic ★★ same type
- TET3 p.Arg1150Ter Pathogenic ★★ same type
- TET3 p.Arg911Gln Likely pathogenic ★★ same type
- TET3 p.Arg1054His Uncertain significance ★★ ⚠ same type
- TET3 p.Arg1688Cys Uncertain significance ★★ ⚠ same type
- TET3 p.Arg1744His Uncertain significance ★★ ⚠ same type
- TET3 p.Arg430Gly Uncertain significance ★★ ⚠ same type
- TET3 p.Arg604Gln 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/tet3-p-val293 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown