ABCB4 p.Phe1011=
c.3033T>C · rs1297237099 · VCV594880
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0117%, amr)
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 0.21 | GERP 0.6, phastCons 0.26 |
| Overall | ||
| CADD | 2.543 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0117%
Admixed American · 7/60,022 alleles
Filtering AF
0.00543%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0038%
Overall
0.00105%
17/1,614,142 alleles · ultra-rare
exomes 17/1,461,826 · genomes 0/152,316 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0117% | 8,575 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,506 |
| European (non-Finnish) | 0.000763% | 131,111 |
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
- Protein
- p.Phe1011=
- Coding
- c.3033T>C
- MANE Select
- NM_000443
- dbSNP
- rs1297237099
- Type
- single nucleotide variant
- Location
- chr7:87409284 (GRCh38)
- Gene constraint
- LOEUF 0.623 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 83.36 · 4 PDB
- Residue 1011
- an α-helix
Similar variants
- ABCB4 c.1006-2A>C Pathogenic ★★ same type
- ABCB4 c.1356+2T>C Pathogenic/Likely pathogenic ★★ same type
- ABCB4 c.1560+1G>A Likely pathogenic ★★ same type
- ABCB4 c.2064+3A>T Likely pathogenic ★★ same type
- ABCB4 c.2211+1G>A Pathogenic/Likely pathogenic ★★ same type
- ABCB4 c.2682+1G>A Pathogenic/Likely pathogenic ★★ same type
- ABCB4 c.2783+1G>T Pathogenic/Likely pathogenic ★★ same type
- ABCB4 c.286+1G>A Pathogenic ★★ 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/abcb4-p-phe1011 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown