CD163 p.Cys1008=
c.3024T>C · rs78817356 · VCV784232
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 7.76%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.412 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.85 | GERP -3.7, phastCons 0.97 |
| Overall | ||
| CADD | 6.618 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
7.76%
African / African-American · 5,818/74,994 alleles
Filtering AF
7.59%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 7.52%
Overall
0.414%
6,690/1,614,072 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 7.76% | 13 |
| Admixed American | 0.618% | 162 |
| Remaining individualsnot grpmax-eligible | 0.542% | 184 |
| Middle Eastern | 0.198% | 505 |
| South Asian | 0.0143% | 7,006 |
| European (non-Finnish) | 0.0112% | 8,939 |
| Finnishnot grpmax-eligible | 0.00625% | 16,009 |
| East Asian | 0.00223% | 44,860 |
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.Cys1008=
- Coding
- c.3024T>C
- MANE Select
- NM_203416
- dbSNP
- rs78817356
- Type
- single nucleotide variant
- Location
- chr12:7483431 (GRCh38)
- Gene constraint
- LOEUF 0.56 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.72 · 14 PDB
- Residue 1008
- the srcr 9 domain; a disulfide bond
Similar variants
- 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.Ile342Val Benign ★★ ⚠ same type
- CD163 p.Leu867= Benign ★★ same type
- CD163 p.Ser570Asn 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-cys1008 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown