Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 5.55%, 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. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.65 | GERP 0.72, phastCons 0.6 |
| Overall | ||
| CADD | 8.42 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.55%
African / African-American · 4,159/74,946 alleles
Filtering AF
5.41%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.35%
Overall
0.289%
4,663/1,613,314 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.55% | 18 |
| Remaining individualsnot grpmax-eligible | 0.371% | 269 |
| Admixed American | 0.294% | 341 |
| Middle Eastern | 0.0991% | 1,009 |
| European (non-Finnish) | 0.00721% | 13,877 |
| South Asian | 0.00549% | 18,208 |
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
- CD164
- Protein
- p.Thr134=
- Coding
- c.402A>G
- MANE Select
- NM_006016
- dbSNP
- rs9480941
- Type
- single nucleotide variant
- Location
- chr6:109370436 (GRCh38)
- Gene constraint
- LOEUF 1.232 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 67.15
- Residue 134
- the 'disordered' region
Similar variants
- CD164 p.Thr134Ala Uncertain significance ★★ ⚠ same residue
- CD164 p.Arg192Ter Uncertain significance ★★ same type
- CD164 p.Asn121Ser Uncertain significance ★★ ⚠ same type
- CD164 p.Asn32Lys Uncertain significance ★★ ⚠ same type
- CD164 p.Asp107Asn Uncertain significance ★★ ⚠ same type
- CD164 p.Leu15Val Uncertain significance ★★ ⚠ same type
- CD164 p.Leu183Pro Uncertain significance ★★ ⚠ same type
- CD164 p.Leu9Phe 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/cd164-p-thr134 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown