CD70 p.Ser141=
c.423C>T · rs34080876 · VCV2672737
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.03%, 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 1.9 | GERP -0.79, phastCons 1 |
| Overall | ||
| CADD | 4.103 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.03%
African / African-American · 771/75,042 alleles
Filtering AF
0.967%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.943%
Overall
0.0545%
879/1,614,158 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.03% | 97 |
| Admixed American | 0.085% | 1,177 |
| Middle Eastern | 0.066% | 1,515 |
| Remaining individualsnot grpmax-eligible | 0.064% | 1,563 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
| South Asian | 0.0011% | 91,082 |
| European (non-Finnish) | 0.000932% | 107,275 |
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.Ser141=
- Coding
- c.423C>T
- MANE Select
- NM_001252
- dbSNP
- rs34080876
- Type
- single nucleotide variant
- Location
- chr19:6586179 (GRCh38)
- Gene constraint
- LOEUF 1.251 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.52 · 1 PDB
- Residue 141
- the thd domain; a β-strand; a disulfide bond
Similar variants
- 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
- CD70 p.Cys115= Benign ★★ same type
- CD70 p.Gly16= Likely 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/cd70-p-ser141 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown