ABCC5 p.Ser900=
c.2700G>A · rs28365026 · VCV2654301
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.429%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.026 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.6 | GERP -4.4 |
| Overall | ||
| CADD | 5.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.429%
European (non-Finnish) · 5,061/1,178,750 alleles
Filtering AF
0.419%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.415%
Overall
0.355%
5,725/1,612,500 alleles · rare
exomes 5,351/1,460,262 · genomes 374/152,238 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.429% | 233 |
| Remaining individualsnot grpmax-eligible | 0.327% | 306 |
| Middle Eastern | 0.297% | 336 |
| Admixed American | 0.218% | 458 |
| Finnishnot grpmax-eligible | 0.206% | 484 |
| South Asian | 0.13% | 772 |
| African / African-American | 0.076% | 1,316 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,799 |
| East Asian | 0.00446% | 22,413 |
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
- ABCC5
- Protein
- p.Ser900=
- Coding
- c.2700G>A
- MANE Select
- NM_005688
- dbSNP
- rs28365026
- Type
- single nucleotide variant
- Location
- chr3:183951971 (GRCh38)
- Gene constraint
- LOEUF 0.455 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 78.13 · 6 PDB
- Residue 900
- a β-strand; the abc transmembrane type-1 2 domain
Similar variants
- ABCC5 p.Ser900Leu Uncertain significance ★ ⚠ same residue
- ABCC5 c.825+10G>A Benign ★★ same type
- ABCC5 p.Cys594= Benign ★★ same type
- ABCC5 p.Ala1008Ser Uncertain significance ★ ⚠ same type
- ABCC5 p.Ala1150Thr Uncertain significance ★ ⚠ same type
- ABCC5 p.Ala1182Val Uncertain significance ★ ⚠ same type
- ABCC5 p.Ala1302Gly Uncertain significance ★ ⚠ same type
- ABCC5 p.Ala1343Thr Uncertain significance ★ ⚠ 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/abcc5-p-ser900 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown