ABCA3 p.Ser693=
c.2079G>A · rs977720309 · VCV2895241
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0107%, afr)
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 -16 | GERP -5.4 |
| Overall | ||
| CADD | 0.751 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0107%
African / African-American · 8/74,894 alleles
Filtering AF
0.00528%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00381%
Overall
0.00105%
17/1,612,784 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0107% | 9,362 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,424 |
| South Asian | 0.0011% | 91,060 |
| European (non-Finnish) | 0.000593% | 168,568 |
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
- ABCA3
- Protein
- p.Ser693=
- Coding
- c.2079G>A
- MANE Select
- NM_001089
- dbSNP
- rs977720309
- Type
- single nucleotide variant
- Location
- chr16:2297513 (GRCh38)
- Gene constraint
- LOEUF 0.612 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.00 · 2 PDB
- Residue 693
- a β-strand; the abc transporter 1 domain
Similar variants
- ABCA3 p.Ser693Leu Uncertain significance ★★ ⚠ same residue
- ABCA3 c.1112-20G>A Likely pathogenic ★★ same type
- ABCA3 c.2053-1G>C Likely pathogenic ★★ same type
- ABCA3 c.2414+1G>A Likely pathogenic ★★ same type
- ABCA3 c.3863-98C>T Pathogenic ★★ same type
- ABCA3 c.614-2A>G Likely pathogenic ★★ same type
- ABCA3 p.Ala1070Thr Likely pathogenic ★★ ⚠ same type
- ABCA3 p.Arg1550Trp 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/abca3-p-ser693 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown