ABCC2 c.468+13del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.279%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +13 | near-intronic (+13 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 2.1 | GERP 0.62, phastCons 1 |
| Non-coding constraint | Z 0.79 | 1 kb window · o/e 0.94 · regional · uncalibrated |
| Overall | ||
| CADD | 3.14 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.279%
Middle Eastern · 17/6,084 alleles
Filtering AF
0.178%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.146%
Overall
0.00626%
101/1,613,818 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.279% | 358 |
| South Asian | 0.0626% | 1,598 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,942 |
| European (non-Finnish) | 0.00153% | 65,554 |
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
- ABCC2
- Coding
- c.468+13del
- MANE Select
- NM_000392
- dbSNP
- rs747293124
- Type
- Deletion
- Location
- chr10:99793692 (GRCh38)
- Gene constraint
- LOEUF 0.985 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.40 · 16 PDB
Similar variants
- ABCC2 p.Asn159fs Pathogenic ★★ same type
- ABCC2 p.Asn718fs Pathogenic/Likely pathogenic ★★ same type
- ABCC2 p.Ile754fs Pathogenic ★★ same type
- ABCC2 p.Leu431fs Pathogenic ★★ same type
- ABCC2 p.Leu788fs Pathogenic/Likely pathogenic ★★ same type
- ABCC2 p.Leu809fs Pathogenic/Likely pathogenic ★★ same type
- ABCC2 p.Pro194_Ser195insTer Pathogenic ★★ same type
- ABCC2 p.Pro274fs 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/abcc2-c-468-plus-13del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown