BAHCC1 p.Pro532=
c.1596G>A · rs782701798 · VCV2648449
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0388%, eas)
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 -8.8 | GERP -2.5 |
| Overall | ||
| CADD | 0.351 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0388%
East Asian · 16/41,244 alleles
Filtering AF
0.0243%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0198%
Overall
0.00437%
34/778,922 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0388% | 2,578 |
| African / African-American | 0.00676% | 14,783 |
| South Asian | 0.00536% | 18,654 |
| Finnishnot grpmax-eligible | 0.00482% | 20,752 |
| Remaining individualsnot grpmax-eligible | 0.00285% | 35,080 |
| European (non-Finnish) | 0.00144% | 69,638 |
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
- BAHCC1
- Protein
- p.Pro532=
- Coding
- c.1596G>A
- MANE Select
- NM_001377448
- dbSNP
- rs782701798
- Type
- single nucleotide variant
- Location
- chr17:81442945 (GRCh38)
- Gene constraint
- LOEUF 1.959 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 40.51
Similar variants
- BAHCC1 p.Ala27Ser Uncertain significance ★ ⚠ same type
- BAHCC1 p.Arg16His Uncertain significance ★ ⚠ same type
- BAHCC1 p.Trp831Ter Uncertain significance ★ same type
- BAHCC1 p.Ala1035Thr Likely benign ★ same type
- BAHCC1 p.Ala1813= Likely benign ★ same type
- BAHCC1 p.Arg770Leu Likely benign ★ ⚠ same type
- BAHCC1 p.Gly2305= Likely benign ★ same type
- BAHCC1 p.Gly2399= 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/bahcc1-p-pro532 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown