CD163 p.Ala15=
c.45T>A · rs1470715220 · VCV2431073
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000515%, nfe)
Conditions
1
lung adenocarcinoma
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.25 | donor loss, 42 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.01 | GERP -2.7, phastCons 0.012 |
| Overall | ||
| CADD | 7.947 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000515%
European (non-Finnish) · 6/1,165,246 alleles
Filtering AF
0.000185%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000122%
Overall
0.000416%
6/1,441,832 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
- CD163
- Protein
- p.Ala15=
- Coding
- c.45T>A
- MANE Select
- NM_203416
- dbSNP
- rs1470715220
- Type
- single nucleotide variant
- Location
- chr12:7503646 (GRCh38)
- Gene constraint
- LOEUF 0.56 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.72 · 14 PDB
Similar variants
- CD163 c.3344-144C>G Uncertain significance ★ same condition
- CD163 c.3344-24C>A Benign ★★ same type
- CD163 c.3344-56G>A Likely benign ★★ same type
- CD163 c.457+9T>A Benign ★★ same type
- CD163 p.Asn642Lys Benign ★★ same type
- CD163 p.Asn892= Benign ★★ same type
- CD163 p.Cys1008= Benign ★★ same type
- CD163 p.Ile342Val 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/cd163-p-ala15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown