IL10 p.Asp43=
c.129T>C · VCV4748948
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Conditions
1
inflammatory bowel disease
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 -0.13 | GERP -3.4, phastCons 0.46 |
| Overall | ||
| CADD | 6.201 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,024 alleles
Overall
6.2e-05%
1/1,614,204 alleles · very rare
exomes 1/1,461,864 · genomes 0/152,340 · 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
- IL10
- Protein
- p.Asp43=
- Coding
- c.129T>C
- MANE Select
- NM_000572
- Type
- single nucleotide variant
- Location
- chr1:206772307 (GRCh38)
- Gene constraint
- LOEUF 0.711 · pLI 0.48 (gnomAD)
- Structure
- AlphaFold pLDDT 88.89 · 9 PDB
- Residue 43
- an α-helix
Similar variants
- IL10 c.225+6A>G Uncertain significance ★★ same condition
- IL10 p.Arg124Trp Uncertain significance ★★ ⚠ same condition
- IL10 p.Arg177Ter Uncertain significance ★★ same condition
- IL10 p.Glu169Asp Uncertain significance ★★ ⚠ same condition
- IL10 p.Leu13Met Uncertain significance ★★ ⚠ same condition
- IL10 c.165+20G>A Likely benign ★★ same condition
- IL10 c.165+8T>C Benign/Likely benign ★★ same condition
- IL10 c.166-15T>C Benign/Likely benign ★★ same condition
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/il10-p-asp43 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown