Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 5.1%, afr) — too common for a highly-penetrant pathogenic allele
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 · G>C here scores Δ0.92 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP -4.6, phastCons 0.68 |
| Overall | ||
| CADD | 7.042 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.1%
African / African-American · 3,826/74,986 alleles
Filtering AF
4.97%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.91%
Overall
0.272%
4,393/1,614,080 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.1% | 20 |
| Admixed American | 0.4% | 250 |
| Remaining individualsnot grpmax-eligible | 0.384% | 260 |
| Middle Eastern | 0.231% | 433 |
| South Asian | 0.00988% | 10,120 |
| European (non-Finnish) | 0.00542% | 18,438 |
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.Asp326=
- Coding
- c.978C>T
- MANE Select
- NM_004613
- dbSNP
- rs2229471
- Type
- single nucleotide variant
- Location
- chr20:38142081 (GRCh38)
- Gene constraint
- LOEUF 0.902 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.91 · 14 PDB
- Residue 326
- a disulfide bond
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.Ile416= Benign ★★ same type
- TGM2 p.Pro217= 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-asp326 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown