ABCB7 p.Thr246=
c.738G>A · rs150594123 · VCV2051259
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00876%, 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 -1 | GERP -3.3, phastCons 0.005 |
| Overall | ||
| CADD | 1.811 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00876%
African / African-American · 5/57,075 alleles
Filtering AF
0.00709%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00656%
Overall
0.00744%
90/1,209,496 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00876% | 11,415 |
| European (non-Finnish) | 0.00871% | 11,475 |
| Remaining individualsnot grpmax-eligible | 0.0063% | 15,866 |
| East Asian | 0.00593% | 16,867 |
| South Asian | 0.00352% | 28,401 |
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.Thr246=
- Coding
- c.738G>A
- MANE Select
- NM_001271696
- dbSNP
- rs150594123
- Type
- single nucleotide variant
- Location
- chrX:75075479 (GRCh38)
- Structure
- AlphaFold pLDDT 78.19 · 4 PDB
- Residue 246
- the abc transmembrane type-1 domain
Similar variants
- 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
- ABCB7 p.Glu494Gln Uncertain significance ★★ ⚠ same type
- ABCB7 p.Gly197Cys 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-thr246 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown