Is ABCB11 c.2011+87A>C pathogenic?

ABCB11 c.2011+87A>C is classified Likely benign in ABCB11 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2020-10-29). Low-frequency (popmax 1.19%, nfe).

How common is ABCB11 c.2011+87A>C in the general population?

ABCB11 c.2011+87A>C is low-frequency (popmax 1.19%, nfe) (gnomAD).

ABCB11 c.2011+87A>C

rs142345608 · VCV1179582

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.19%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +87	deep intronic (+87 nt into the intron)
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.25	GERP -2.4
Overall
CADD	4.377	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.19% European (non-Finnish) · 10,526/883,344 alleles

Filtering AF 1.17% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.16%

Overall 0.978% 12,146/1,241,380 alleles · low-frequency

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	3.51%	29
Ashkenazi Jewishnot grpmax-eligible	1.38%	72
European (non-Finnish)grpmax	1.19%	84
Remaining individualsnot grpmax-eligible	0.823%	121
Middle Eastern	0.761%	131
Finnishnot grpmax-eligible	0.489%	204
Admixed American	0.369%	271
South Asian	0.341%	293
African / African-American	0.179%	560
East Asian	0.00254%	39,304

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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+87A>C
MANE Select: NM_003742
dbSNP: rs142345608
Type: single nucleotide variant
Location: chr2:168969263 (GRCh38)
Gene constraint: LOEUF 0.739 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 83.23 · 9 PDB

Full ABCB11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABCB11 c.1084-2A>G Pathogenic ★★ same type
ABCB11 c.1197+1G>T Pathogenic/Likely pathogenic ★★ same type
ABCB11 c.1198-1G>C Pathogenic/Likely pathogenic ★★ same type
ABCB11 c.1198-2A>C Likely pathogenic ★★ same type
ABCB11 c.1435-2A>T Pathogenic/Likely pathogenic ★★ same type
ABCB11 c.150+1G>A Pathogenic/Likely pathogenic ★★ same type
ABCB11 c.150+2T>C Pathogenic/Likely pathogenic ★★ same type
ABCB11 c.150+3A>C Pathogenic/Likely 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-87a-c (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown