ABCA2 p.Arg1514=
c.4542C>T · rs201649376 · VCV3044326
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.138%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.94 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.70 | gain · loss 0.22 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -1.8 | GERP -2.8 |
| Overall | ||
| CADD | 20.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.138%
European (non-Finnish) · 1,625/1,177,806 alleles
Filtering AF
0.132%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.13%
Overall
0.109%
1,751/1,605,688 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.138% | 725 |
| Remaining individualsnot grpmax-eligible | 0.0948% | 1,055 |
| Finnishnot grpmax-eligible | 0.0666% | 1,501 |
| African / African-American | 0.0173% | 5,767 |
| East Asian | 0.00897% | 11,152 |
| South Asian | 0.00894% | 11,180 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00342% | 29,252 |
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
- ABCA2
- Protein
- p.Arg1514=
- Coding
- c.4542C>T
- MANE Select
- NM_001606
- dbSNP
- rs201649376
- Type
- single nucleotide variant
- Location
- chr9:137013469 (GRCh38)
- Gene constraint
- LOEUF 0.436 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 71.46
- Residue 1514
- a UniProt-annotated variant site (in idpogsa)
Similar variants
- ABCA2 p.Arg1514His Conflicting classifications of pathogenicity ★ ⚠ same residue
- ABCA2 p.Arg1514Ser Uncertain significance ★ ⚠ same residue
- ABCA2 p.Gln1370Ter Likely pathogenic ★★ same type
- ABCA2 c.3883-3C>T Uncertain significance ★★ same type
- ABCA2 p.Ala1357Thr Uncertain significance ★★ ⚠ same type
- ABCA2 p.Ala1620Thr Uncertain significance ★★ ⚠ same type
- ABCA2 p.Ala1645Val Uncertain significance ★★ ⚠ same type
- ABCA2 p.Ala1715Ser 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/abca2-p-arg1514 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown