BACH2 p.Glu164del
c.486GGA[2] · rs754304276 · VCV1391711
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000508%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5 | GERP -3.6 |
| Region caveats | ||
| Repeat context | tandem | (CTC)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000508%
European (non-Finnish) · 6/1,179,994 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.00041%
6/1,461,882 alleles · very rare
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
- BACH2
- Protein
- p.Glu164del
- Coding
- c.486GGA[2]
- MANE Select
- NM_021813
- dbSNP
- rs754304276
- Type
- Microsatellite
- Location
- chr6:89951612 (GRCh38)
- Gene constraint
- LOEUF 0.164 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.66 · 2 PDB
- Residue 164
- the 'disordered' region
Similar variants
- BACH2 p.Glu164Asp Uncertain significance ★ ⚠ same residue
- BACH2 p.Arg795del Uncertain significance ★ same type
- BACH2 p.Phe433del Uncertain significance ★ same type
- BACH2 p.Ser247del Uncertain significance ★ same type
- BACH2 p.Ser436del Uncertain significance ★ same type
- BACH2 c.2044-21_2044-20del Likely benign ★ same type
- BACH2 c.-12-18TTTC[3] Likely benign ★ same type
- BACH2 c.-12-18TTTC[5] Likely 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/bach2-p-glu164del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown