ABCB11 c.2011+218del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 8.68%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +218 | deep intronic (+218 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -5.1 | GERP 1.2 |
| Overall | ||
| CADD | 0.398 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.68%
African / African-American · 2,819/32,460 alleles
Filtering AF
8.42%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 8.31%
Overall
3.97%
5,270/132,656 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 8.68% | 12 |
| Middle Eastern | 4.04% | 25 |
| Remaining individualsnot grpmax-eligible | 3.83% | 26 |
| Finnishnot grpmax-eligible | 3.5% | 29 |
| Admixed American | 2.71% | 37 |
| European (non-Finnish) | 2.54% | 39 |
| Ashkenazi Jewishnot grpmax-eligible | 1.73% | 58 |
| South Asian | 1.33% | 75 |
| East Asian | 0.129% | 776 |
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
- ABCB11
- Coding
- c.2011+218del
- MANE Select
- NM_003742
- dbSNP
- rs35908291
- Type
- Deletion
- Location
- chr2:168969132 (GRCh38)
- Gene constraint
- LOEUF 0.739 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 83.23 · 9 PDB
Similar variants
- ABCB11 c.3213+1del Pathogenic ★★ same type
- ABCB11 p.Ala452fs Pathogenic ★★ same type
- ABCB11 p.Arg830fs Pathogenic ★★ same type
- ABCB11 p.Asn199fs Pathogenic/Likely pathogenic ★★ same type
- ABCB11 p.Asp848fs Pathogenic/Likely pathogenic ★★ same type
- ABCB11 p.Gln1058fs Pathogenic ★★ same type
- ABCB11 p.Gly1267fs Likely pathogenic ★★ same type
- ABCB11 p.Gly648fs 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/abcb11-c-2011-plus-218del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown