ABCB7 p.His588=
c.1764T>C · rs150273961 · VCV517092
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.308%, 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 3 | GERP 0.47, phastCons 1 |
| Overall | ||
| CADD | 9.899 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.308%
African / African-American · 176/57,156 alleles
Filtering AF
0.271%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.256%
Overall
0.0179%
217/1,209,358 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.308% | 325 |
| Middle Eastern | 0.046% | 2,175 |
| Admixed American | 0.0351% | 2,851 |
| Remaining individualsnot grpmax-eligible | 0.0336% | 2,974 |
| South Asian | 0.00176% | 56,756 |
| European (non-Finnish) | 0.00067% | 149,148 |
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
- ABCB7
- Protein
- p.His588=
- Coding
- c.1764T>C
- MANE Select
- NM_001271696
- dbSNP
- rs150273961
- Type
- single nucleotide variant
- Location
- chrX:75065137 (GRCh38)
- Structure
- AlphaFold pLDDT 78.19 · 4 PDB
- Residue 588
- the abc transporter domain; an α-helix
Similar variants
- ABCB7 p.His588Arg Uncertain significance ★ same residue
- ABCB7 p.His588Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
- ABCB7 c.1659+5T>G Uncertain significance ★★ same type
- ABCB7 c.1935+5G>C Uncertain significance ★★ same type
- ABCB7 p.Ala5Glu Uncertain significance ★★ ⚠ same type
- ABCB7 p.Arg711His Uncertain significance ★★ ⚠ same type
- ABCB7 p.Asn378Asp Uncertain significance ★★ ⚠ same type
- ABCB7 p.Asp653Asn 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/abcb7-p-his588 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown