CD70 p.Thr159=
c.477G>A · rs778323980 · VCV3047880
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00178%, nfe)
Conditions
1
CD70-related disorder
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 -8 | GERP -2.8 |
| Overall | ||
| CADD | 0.142 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00178%
European (non-Finnish) · 21/1,179,982 alleles
Filtering AF
0.00114%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000971%
Overall
0.00143%
23/1,613,946 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00178% | 56,190 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,480 |
| South Asian | 0.0011% | 91,082 |
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
- CD70
- Protein
- p.Thr159=
- Coding
- c.477G>A
- MANE Select
- NM_001252
- dbSNP
- rs778323980
- Type
- single nucleotide variant
- Location
- chr19:6586125 (GRCh38)
- Gene constraint
- LOEUF 1.251 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.52 · 1 PDB
- Residue 159
- the thd domain; a β-strand; a disulfide bond
Disease context
CD70-related disorder
Similar variants
- CD70 p.Thr159Met Uncertain significance ★ ⚠ same residue
- CD70 p.Leu151= Likely benign same condition
- CD70 p.Leu23Phe Uncertain significance ★★ ⚠ same type
- CD70 p.Ser146Ile Uncertain significance ★★ ⚠ same type
- CD70 p.Ser9Leu Uncertain significance ★★ ⚠ same type
- CD70 p.Thr118Met Uncertain significance ★★ ⚠ same type
- CD70 p.Thr119Met Uncertain significance ★★ ⚠ same type
- CD70 p.Val130Met 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/cd70-p-thr159 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown