ABCA5 p.Val103=
c.309C>T · rs773593014 · VCV2648168
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000174%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.71 | GERP -3.2 |
| Overall | ||
| CADD | 0.15 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000174%
European (non-Finnish) · 2/1,148,420 alleles
Filtering AF
2.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000129%
2/1,550,614 alleles · very rare
exomes 2/1,398,362 · genomes 0/152,252 · joint denominator
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.Val103=
- Coding
- c.309C>T
- MANE Select
- NM_172232
- dbSNP
- rs773593014
- Type
- single nucleotide variant
- Location
- chr17:69309422 (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-val103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown