ABCA1 p.Arg219=
c.655A>C · rs778562903 · VCV2577057
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0483%, 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 0.81 | GERP -1.8 |
| Overall | ||
| CADD | 6.277 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0483%
South Asian · 44/91,086 alleles
Filtering AF
0.0369%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.033%
Overall
0.00315%
46/1,461,874 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0483% | 2,070 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,255 |
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
- ABCA1
- Protein
- p.Arg219=
- Coding
- c.655A>C
- MANE Select
- NM_005502
- dbSNP
- rs778562903
- Type
- single nucleotide variant
- Location
- chr9:104858587 (GRCh38)
- Gene constraint
- LOEUF 0.563 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.50 · 7 PDB
- Residue 219
- an α-helix; a disulfide bond; a UniProt-annotated variant site (in)
Similar variants
- ABCA1 p.Arg219Lys Benign ★★ same residue
- ABCA1 c.4175+1G>T Pathogenic/Likely pathogenic ★★ same type
- ABCA1 c.4274+1G>A Likely pathogenic ★★ same type
- ABCA1 c.5237+3A>C Likely pathogenic ★★ same type
- ABCA1 p.Arg2080Trp Likely pathogenic ★★ same type
- ABCA1 p.Arg557Ter Pathogenic/Likely pathogenic ★★ same type
- ABCA1 p.Arg587Trp Pathogenic/Likely pathogenic ★★ same type
- ABCA1 p.Asn1800His Pathogenic/Likely 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/abca1-p-arg219 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown