ABCA3 p.Ser1516=
c.4548T>C · rs150953197 · VCV2143422
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.206%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>T here scores Δ0.65 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -12 | GERP -5 |
| Overall | ||
| CADD | 0.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.206%
South Asian · 188/91,086 alleles
Filtering AF
0.182%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.173%
Overall
0.0124%
200/1,611,600 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.206% | 485 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,681 |
| African / African-American | 0.00133% | 75,042 |
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.Ser1516=
- Coding
- c.4548T>C
- MANE Select
- NM_001089
- dbSNP
- rs150953197
- Type
- single nucleotide variant
- Location
- chr16:2278458 (GRCh38)
- Gene constraint
- LOEUF 0.612 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.00 · 2 PDB
- Residue 1516
- the abc transporter 2 domain
Similar variants
- ABCA3 p.Ser1516Asn 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-ser1516 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown