ABCA12 p.Ala2403=
c.7209C>G · rs746403011 · VCV2057085
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0582%, sas)
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 1.9 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 5.678 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0582%
South Asian · 53/91,068 alleles
Filtering AF
0.0457%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0412%
Overall
0.00644%
104/1,613,790 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0582% | 1,718 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,494 |
| Admixed American | 0.00667% | 15,000 |
| European (non-Finnish) | 0.00356% | 28,092 |
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
- ABCA12
- Protein
- p.Ala2403=
- Coding
- c.7209C>G
- MANE Select
- NM_173076
- dbSNP
- rs746403011
- Type
- single nucleotide variant
- Location
- chr2:214947452 (GRCh38)
- Gene constraint
- LOEUF 0.582 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.32
- Residue 2403
- the abc transporter 2 domain; a UniProt-annotated variant site (in arci4b); a UniProt-annotated variant site (in arci4b; uncertain significance)
Similar variants
- ABCA12 c.2592+1G>A Likely pathogenic ★★ same type
- ABCA12 c.5381+1G>C Pathogenic/Likely pathogenic ★★ same type
- ABCA12 c.985+1G>A Likely pathogenic ★★ same type
- ABCA12 p.Arg1297Ter Pathogenic ★★ same type
- ABCA12 p.Arg1514Cys Pathogenic ★★ same type
- ABCA12 p.Arg1514His Pathogenic/Likely pathogenic ★★ same type
- ABCA12 p.Arg1515Ter Pathogenic ★★ same type
- ABCA12 p.Arg1950Ter Pathogenic ★★ 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/abca12-p-ala2403 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown