CXCR6 p.Phe234=
c.702C>T · rs34294191 · VCV716101
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.09%, afr)
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 -0.49 | GERP -1.7, phastCons 0.031 |
| Overall | ||
| CADD | 6.541 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.09%
African / African-American · 3,073/75,044 alleles
Filtering AF
3.97%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.93%
Overall
0.226%
3,645/1,614,188 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.09% | 24 |
| Admixed American | 0.378% | 264 |
| Remaining individualsnot grpmax-eligible | 0.326% | 306 |
| Middle Eastern | 0.182% | 551 |
| European (non-Finnish) | 0.0106% | 9,440 |
| South Asian | 0.00439% | 22,770 |
| East Asian | 0.00223% | 44,882 |
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
- CXCR6
- Protein
- p.Phe234=
- Coding
- c.702C>T
- MANE Select
- NM_006564
- dbSNP
- rs34294191
- Type
- single nucleotide variant
- Location
- chr3:45947183 (GRCh38)
- Gene constraint
- LOEUF 1.476 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.16
Similar variants
- CXCR6 p.Asp184= Benign/Likely benign ★★ same type
- CXCR6 p.Asp77= Likely benign ★★ same type
- CXCR6 p.Ala221Thr Uncertain significance ★ ⚠ same type
- CXCR6 p.Arg127His Uncertain significance ★ ⚠ same type
- CXCR6 p.Arg254Cys Uncertain significance ★ ⚠ same type
- CXCR6 p.Asn333Ser Uncertain significance ★ ⚠ same type
- CXCR6 p.Asp323Glu Uncertain significance ★ ⚠ same type
- CXCR6 p.Asp9Ala 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/cxcr6-p-phe234 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown