NT5E p.Ile308=
c.924T>C · rs141102470 · VCV754702
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0128%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.008 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.5 | GERP 0.24, phastCons 1 |
| Overall | ||
| CADD | 8.473 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0128%
European (non-Finnish) · 151/1,180,032 alleles
Filtering AF
0.0111%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0105%
Overall
0.0096%
155/1,614,108 alleles · ultra-rare
exomes 151/1,461,860 · genomes 4/152,248 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0128% | 7,815 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,622 |
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
- NT5E
- Protein
- p.Ile308=
- Coding
- c.924T>C
- MANE Select
- NM_002526
- dbSNP
- rs141102470
- Type
- single nucleotide variant
- Location
- chr6:85485407 (GRCh38)
- Gene constraint
- LOEUF 1.254 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.95 · 52 PDB
Similar variants
- NT5E c.1210+12G>C Benign ★★ same type
- NT5E p.Gly148= Likely benign ★★ same type
- NT5E p.Thr376Ala Benign ★★ same type
- NT5E p.Thr407= Benign/Likely benign ★★ same type
- NT5E c.1104+2T>A Likely pathogenic ★ same type
- NT5E p.Cys476Ter Likely pathogenic ★ same type
- NT5E c.562+1G>T Uncertain significance ★ same type
- NT5E p.Ala10Pro 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/nt5e-p-ile308 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown