BAHCC1 p.Pro1884=
c.5652C>T · rs61744534 · VCV2648454
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.271%, mid)
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 -14 | GERP -3 |
| Overall | ||
| CADD | 0.229 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.271%
Middle Eastern · 12/4,428 alleles
Filtering AF
0.156%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.136%
Overall
0.105%
812/771,080 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.271% | 369 |
| European (non-Finnish) | 0.15% | 666 |
| South Asian | 0.116% | 863 |
| Remaining individualsnot grpmax-eligible | 0.112% | 892 |
| Admixed American | 0.0482% | 2,077 |
| African / African-American | 0.022% | 4,543 |
| Finnishnot grpmax-eligible | 0.0181% | 5,537 |
| East Asian | 0.0049% | 20,394 |
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.Pro1884=
- Coding
- c.5652C>T
- MANE Select
- NM_001377448
- dbSNP
- rs61744534
- Type
- single nucleotide variant
- Location
- chr17:81459100 (GRCh38)
- Gene constraint
- LOEUF 1.959 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 40.51
- Residue 1884
- the 'disordered' region
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-pro1884 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown