CD7 p.Pro39=
c.117C>T · VCV4650695
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0681%, 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 -15 | GERP -2.8 |
| Overall | ||
| CADD | 0.086 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0681%
African / African-American · 51/74,894 alleles
Filtering AF
0.0532%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0479%
Overall
0.00405%
65/1,603,796 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0681% | 1,469 |
| East Asian | 0.00892% | 11,216 |
| Admixed American | 0.00334% | 29,925 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,155 |
| South Asian | 0.0011% | 90,772 |
| European (non-Finnish) | 0.000424% | 235,690 |
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
- CD7
- Protein
- p.Pro39=
- Coding
- c.117C>T
- MANE Select
- NM_006137
- Type
- single nucleotide variant
- Location
- chr17:82316947 (GRCh38)
- Gene constraint
- LOEUF 1.673 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.51 · 2 PDB
- Residue 39
- a disulfide bond; the ig-like domain
Similar variants
- CD7 p.Ala145Thr Uncertain significance ★ ⚠ same type
- CD7 p.Ala154Asp Uncertain significance ★ ⚠ same type
- CD7 p.Ala154Thr Uncertain significance ★ ⚠ same type
- CD7 p.Ala15Val Uncertain significance ★ ⚠ same type
- CD7 p.Ala17Ser Uncertain significance ★ ⚠ same type
- CD7 p.Ala184Val Uncertain significance ★ ⚠ same type
- CD7 p.Ala217Thr Uncertain significance ★ ⚠ same type
- CD7 p.Ala218Thr 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/cd7-p-pro39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown