Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.79%, 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 -4.3 | GERP -3.9 |
| Overall | ||
| CADD | 0.594 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.79%
African / African-American · 2,835/74,878 alleles
Filtering AF
3.67%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.62%
Overall
0.215%
3,418/1,592,258 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.79% | 26 |
| Admixed American | 0.279% | 359 |
| Remaining individualsnot grpmax-eligible | 0.272% | 368 |
| Middle Eastern | 0.266% | 376 |
| European (non-Finnish) | 0.0204% | 4,895 |
| South Asian | 0.00573% | 17,462 |
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
- TGM2
- Protein
- p.Pro641=
- Coding
- c.1923C>T
- MANE Select
- NM_004613
- dbSNP
- rs2229472
- Type
- single nucleotide variant
- Location
- chr20:38130360 (GRCh38)
- Gene constraint
- LOEUF 0.902 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.91 · 14 PDB
Similar variants
- TGM2 c.433+3G>A Likely benign ★★ same type
- TGM2 p.Ala282= Benign ★★ same type
- TGM2 p.Ala390= Benign ★★ same type
- TGM2 p.Arg28= Benign ★★ same type
- TGM2 p.Arg377His Benign ★★ ⚠ same type
- TGM2 p.Arg76His Benign ★★ same type
- TGM2 p.Asp326= Benign ★★ same type
- TGM2 p.Ile416= Benign ★★ 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/tgm2-p-pro641 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown