ABCA2 p.Lys1936=
c.5808G>A · rs145591245 · VCV3045894
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.174%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.27 | acceptor loss, 1 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -0.92, phastCons 0.6 |
| Overall | ||
| CADD | 8.018 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.174%
East Asian · 78/44,848 alleles
Filtering AF
0.143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.131%
Overall
0.00875%
141/1,611,926 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.174% | 575 |
| South Asian | 0.0362% | 2,759 |
| African / African-American | 0.0213% | 4,686 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,203 |
| Admixed American | 0.00333% | 29,989 |
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.Lys1936=
- Coding
- c.5808G>A
- MANE Select
- NM_001606
- dbSNP
- rs145591245
- Type
- single nucleotide variant
- Location
- chr9:137011301 (GRCh38)
- Gene constraint
- LOEUF 0.436 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 71.46
- Residue 1936
- a UniProt-annotated variant site (in idpogsa)
Similar variants
- 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
- ABCA2 p.Ala2180Thr Uncertain significance ★★ ⚠ same type
- ABCA2 p.Ala2206Val 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-lys1936 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown