ABCB9 p.Thr703=
c.2109C>T · VCV4110393
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0501%, mid)
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 -6.6 | GERP -5.3 |
| Overall | ||
| CADD | 4.573 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0501%
Middle Eastern · 3/5,988 alleles
Filtering AF
0.0136%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00727%
Overall
0.00154%
24/1,557,570 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0501% | 1,996 |
| African / African-American | 0.00544% | 18,395 |
| Remaining individualsnot grpmax-eligible | 0.00331% | 30,199 |
| South Asian | 0.00237% | 42,210 |
| European (non-Finnish) | 0.00113% | 88,518 |
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
- ABCB9
- Protein
- p.Thr703=
- Coding
- c.2109C>T
- MANE Select
- NM_019625
- Type
- single nucleotide variant
- Location
- chr12:122930103 (GRCh38)
- Gene constraint
- LOEUF 0.796 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.76
- Residue 703
- the abc transporter domain
Similar variants
- ABCB9 p.Ala151Val Uncertain significance ★ ⚠ same type
- ABCB9 p.Ala169Thr Uncertain significance ★ ⚠ same type
- ABCB9 p.Ala364Val Uncertain significance ★ ⚠ same type
- ABCB9 p.Ala368Val Uncertain significance ★ ⚠ same type
- ABCB9 p.Ala447Thr Uncertain significance ★ ⚠ same type
- ABCB9 p.Ala641Ser Uncertain significance ★ ⚠ same type
- ABCB9 p.Ala641Thr Uncertain significance ★ ⚠ same type
- ABCB9 p.Ala64Thr 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/abcb9-p-thr703 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown