NTF4 p.Ala52=
c.156C>T · VCV4943299
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00489%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.053 | phastCons 0.15 |
| Overall | ||
| CADD | 7.004 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00489%
East Asian · 2/40,914 alleles
Filtering AF
0.00081%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000303%
Overall
0.000774%
12/1,550,628 alleles · very rare
exomes 9/1,398,340 · genomes 3/152,288 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00489% | 20,457 |
| Remaining individualsnot grpmax-eligible | 0.00166% | 60,108 |
| European (non-Finnish) | 0.000785% | 127,456 |
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
- NTF4
- Protein
- p.Ala52=
- Coding
- c.156C>T
- MANE Select
- NM_006179
- Type
- single nucleotide variant
- Location
- chr19:49061842 (GRCh38)
- Gene constraint
- LOEUF 1.493 · pLI 0.06 (gnomAD)
- Structure
- AlphaFold pLDDT 78.69 · 3 PDB
Similar variants
- NTF4 c.-12-152C>T Likely benign ★★ same type
- NTF4 c.*110A>G Benign ★★ same type
- NTF4 p.Ala88Val Likely benign ★★ same type
- NTF4 p.Arg68Gln Benign ★★ same type
- NTF4 p.Gln174Arg Likely pathogenic ★ same type
- NTF4 p.Ala127Ser Uncertain significance ★ ⚠ same type
- NTF4 p.Ala172Thr Uncertain significance ★ ⚠ same type
- NTF4 p.Ala54Thr 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/ntf4-p-ala52 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown