ABCB4 c.*29A>C
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, afr)
Conditions
2
familial intrahepatic cholestasis
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 2.6 | GERP -1.1, phastCons 1 |
| Non-coding constraint | Z 0.61 | 1 kb window · o/e 0.95 · regional · uncalibrated |
| Overall | ||
| CADD | 15.68 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/74,990 alleles
Filtering AF
0.000443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000205%
3/1,460,160 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00267% | 37,495 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,442 |
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
- ABCB4
- Coding
- c.*29A>C
- MANE Select
- NM_000443
- Type
- single nucleotide variant
- Location
- chr7:87402067 (GRCh38)
- Gene constraint
- LOEUF 0.623 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 83.36 · 4 PDB
Similar variants
- ABCB4 c.1356+2T>C Pathogenic/Likely pathogenic ★★ same condition
- ABCB4 c.2064+3A>T Likely pathogenic ★★ same condition
- ABCB4 c.2211+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ABCB4 c.2682+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ABCB4 c.2783+1G>T Pathogenic/Likely pathogenic ★★ same condition
- ABCB4 c.286+1G>A Pathogenic ★★ same condition
- ABCB4 c.3081+1G>C Pathogenic ★★ same condition
- ABCB4 c.3486+1G>A Pathogenic/Likely pathogenic ★★ same condition
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/abcb4-c-star-29a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown