Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.521%, 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 -5.7 | |
| Overall | ||
| CADD | 9.427 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.521%
African / African-American · 391/75,044 alleles
Filtering AF
0.478%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.462%
Overall
0.0349%
563/1,614,192 alleles · rare
exomes 333/1,461,876 · genomes 230/152,316 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.521% | 192 |
| Remaining individualsnot grpmax-eligible | 0.0544% | 1,839 |
| Middle Eastern | 0.0495% | 2,021 |
| Admixed American | 0.0333% | 3,001 |
| South Asian | 0.0132% | 7,591 |
| European (non-Finnish) | 0.00847% | 11,800 |
| East Asian | 0.00668% | 14,962 |
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
- GSTM2
- Protein
- p.Arg78=
- Coding
- c.234G>C
- MANE Select
- NM_000848
- dbSNP
- rs2229047
- Type
- single nucleotide variant
- Location
- chr1:109669346 (GRCh38)
- Gene constraint
- LOEUF 1.418 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 98.53 · 11 PDB
- Residue 78
- the gst n-terminal domain; an α-helix
Similar variants
- GSTM2 p.Ala112Thr Uncertain significance ★ ⚠ same type
- GSTM2 p.Ala196Asp Uncertain significance ★ ⚠ same type
- GSTM2 p.Arg108Gly Uncertain significance ★ ⚠ same type
- GSTM2 p.Arg82Gly Uncertain significance ★ ⚠ same type
- GSTM2 p.Asp162Tyr Uncertain significance ★ ⚠ same type
- GSTM2 p.Asp42Asn Uncertain significance ★ ⚠ same type
- GSTM2 p.Gln94His Uncertain significance ★ ⚠ same type
- GSTM2 p.Ile10Phe 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/gstm2-p-arg78 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown