ABCA13 p.Ser2909=
c.8727T>C · VCV3506262
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000256%, nfe)
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 · T>G here scores Δ0.38 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.88 | GERP -2.1, phastCons 0.021 |
| Overall | ||
| CADD | 5.565 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000256%
European (non-Finnish) · 3/1,171,222 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000208%
3/1,444,226 alleles · very rare
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
- ABCA13
- Protein
- p.Ser2909=
- Coding
- c.8727T>C
- MANE Select
- NM_152701
- Type
- single nucleotide variant
- Location
- chr7:48281343 (GRCh38)
- Gene constraint
- LOEUF 1.063 · pLI <0.01 (gnomAD)
Similar variants
- ABCA13 p.Ala1627Val Uncertain significance ★★ ⚠ same type
- ABCA13 p.Ala4240Thr Uncertain significance ★★ ⚠ same type
- ABCA13 c.1263-5C>G Benign/Likely benign ★★ same type
- ABCA13 p.Ala2178Glu Benign ★★ same type
- ABCA13 p.Ala922Thr Benign ★★ same type
- ABCA13 p.Arg4043Cys Benign ★★ same type
- ABCA13 p.Arg4070Cys Benign ★★ same type
- ABCA13 p.Arg4681Gln 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/abca13-p-ser2909 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown