ABCB7 p.Asp538=
c.1614T>C · rs776026399 · VCV2870197
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00358%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>C here scores Δ0.35 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.2 | GERP -2.8, phastCons 1 |
| Overall | ||
| CADD | 6.186 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00358%
European (non-Finnish) · 32/893,634 alleles
Filtering AF
0.00259%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00222%
Overall
0.00281%
34/1,207,949 alleles · very rare
exomes 33/1,096,442 · genomes 1/111,507 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00358% | 27,926 |
| African / African-American | 0.0035% | 28,532 |
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.Asp538=
- Coding
- c.1614T>C
- MANE Select
- NM_001271696
- dbSNP
- rs776026399
- Type
- single nucleotide variant
- Location
- chrX:75069052 (GRCh38)
- Structure
- AlphaFold pLDDT 78.19 · 4 PDB
- Residue 538
- the abc transporter domain; an α-helix
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-asp538 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown