Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Common
common (popmax 11.3%, afr) — too common for a highly-penetrant pathogenic allele
Conditions
1
Dubin-Johnson syndrome
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 4.3 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 9.352 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
11.3%
African / African-American · 8,504/74,996 alleles
Filtering AF
11.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 11.1%
Overall
0.614%
9,906/1,614,124 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 11.3% | 9 |
| Admixed American | 0.863% | 116 |
| Remaining individualsnot grpmax-eligible | 0.856% | 117 |
| Amishnot grpmax-eligible | 0.548% | 182 |
| Middle Eastern | 0.379% | 264 |
| Ashkenazi Jewishnot grpmax-eligible | 0.054% | 1,851 |
| South Asian | 0.0285% | 3,503 |
| European (non-Finnish) | 0.0232% | 4,307 |
| Finnishnot grpmax-eligible | 0.00781% | 12,805 |
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
- ABCC2
- Protein
- p.Glu1470=
- Coding
- c.4410G>A
- MANE Select
- NM_000392
- dbSNP
- rs8187706
- Type
- single nucleotide variant
- Location
- chr10:99850698 (GRCh38)
- Gene constraint
- LOEUF 0.985 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.40 · 16 PDB
- Residue 1470
- an α-helix; the abc transporter 2 domain
Disease context
Dubin-Johnson syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Dubin-Johnson syndrome (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Adult
Similar variants
- ABCC2 c.1031+4A>G Pathogenic/Likely pathogenic ★★ same condition
- ABCC2 c.3258+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ABCC2 c.333+1G>A Likely pathogenic ★★ same condition
- ABCC2 c.3415-1G>A Pathogenic/Likely pathogenic ★★ same condition
- ABCC2 c.3741+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ABCC2 c.3741+1G>T Pathogenic/Likely pathogenic ★★ same condition
- ABCC2 c.576+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ABCC2 p.Arg1066Ter 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/abcc2-p-glu1470 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown