ABCB6 c.*2A>G
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.717%, afr)
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 -0.093 | GERP -0.8, phastCons 0.002 |
| Non-coding constraint | Z 2.69 | 1 kb window · o/e 0.83 · regional · uncalibrated |
| Overall | ||
| CADD | 7.78 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.717%
African / African-American · 538/75,030 alleles
Filtering AF
0.667%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.647%
Overall
0.0371%
598/1,613,738 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.717% | 139 |
| Remaining individualsnot grpmax-eligible | 0.0496% | 2,016 |
| Admixed American | 0.0383% | 2,610 |
| South Asian | 0.0011% | 91,074 |
| European (non-Finnish) | 0.000424% | 235,924 |
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
- ABCB6
- Coding
- c.*2A>G
- MANE Select
- NM_005689
- Type
- single nucleotide variant
- Location
- chr2:219209936 (GRCh38)
- Gene constraint
- LOEUF 0.984 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.17 · 16 PDB
Similar variants
- ABCB6 p.Ala164Thr Uncertain significance ★★ ⚠ same type
- ABCB6 p.Ala57Thr Uncertain significance ★★ ⚠ same type
- ABCB6 p.Ala66Thr Uncertain significance ★★ ⚠ same type
- ABCB6 p.Ala681Thr Uncertain significance ★★ ⚠ same type
- ABCB6 p.Arg135Ser Uncertain significance ★★ ⚠ same type
- ABCB6 p.Arg439Cys Uncertain significance ★★ ⚠ same type
- ABCB6 p.Arg450Gln Uncertain significance ★★ ⚠ same type
- ABCB6 p.Arg685His Uncertain significance ★★ ⚠ 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/abcb6-c-star-2a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown