NT5E p.Ala6=
c.18G>C · rs1201305832 · VCV3048888
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000769%, nfe)
Conditions
1
NT5E-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 -3.3 | GERP -2.8 |
| Overall | ||
| CADD | 5.459 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000769%
European (non-Finnish) · 9/1,169,850 alleles
Filtering AF
0.000362%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000262%
Overall
0.000567%
9/1,588,582 alleles · very rare
exomes 9/1,436,418 · genomes 0/152,164 · joint denominator
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.Ala6=
- Coding
- c.18G>C
- MANE Select
- NM_002526
- dbSNP
- rs1201305832
- Type
- single nucleotide variant
- Location
- chr6:85450157 (GRCh38)
- Gene constraint
- LOEUF 1.254 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.95 · 52 PDB
Disease context
NT5E-related disorder
Similar variants
- NT5E p.Cys476Ter Likely pathogenic ★ same condition
- NT5E p.Asp422Tyr Uncertain significance ★ ⚠ same condition
- NT5E p.Ala280= Likely benign same condition
- NT5E p.Asn526= Likely benign same condition
- NT5E p.Leu426= Likely benign same condition
- NT5E p.Leu501= Likely benign same condition
- NT5E p.Pro482= Likely benign same condition
- NT5E p.Val537fs Likely pathogenic ★★ same condition
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-ala6 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown