ABCA5 p.Ser354=
c.1062G>A · rs143655246 · VCV725471
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.203%, nfe)
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 -8.5 | GERP -2.9 |
| Overall | ||
| CADD | 0.843 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.203%
European (non-Finnish) · 2,386/1,176,060 alleles
Filtering AF
0.196%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.193%
Overall
0.158%
2,531/1,599,072 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.203% | 493 |
| Remaining individualsnot grpmax-eligible | 0.124% | 803 |
| Admixed American | 0.0686% | 1,457 |
| Middle Eastern | 0.0333% | 3,002 |
| African / African-American | 0.0189% | 5,298 |
| Finnishnot grpmax-eligible | 0.0188% | 5,317 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00343% | 29,150 |
| South Asian | 0.00114% | 87,472 |
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
- ABCA5
- Protein
- p.Ser354=
- Coding
- c.1062G>A
- MANE Select
- NM_172232
- dbSNP
- rs143655246
- Type
- single nucleotide variant
- Location
- chr17:69302775 (GRCh38)
- Gene constraint
- LOEUF 0.97 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.12
Similar variants
- ABCA5 p.Ser288Phe Uncertain significance ★★ ⚠ same type
- ABCA5 c.4765+3A>G Likely benign ★★ same type
- ABCA5 p.Asn190Ser Likely benign ★★ ⚠ same type
- ABCA5 p.Asn768Asp Benign ★★ same type
- ABCA5 p.Asp817Tyr Likely benign ★★ ⚠ same type
- ABCA5 p.Gly1159Arg Likely benign ★★ ⚠ same type
- ABCA5 p.Gly128= Benign/Likely benign ★★ same type
- ABCA5 p.Ile1173Val Likely benign ★★ 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/abca5-p-ser354 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown