Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 100%, eas) — too common for a highly-penetrant pathogenic allele
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 -20 | GERP -3.2 |
| Overall | ||
| CADD | 0.179 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
100%
East Asian · 44,870/44,886 alleles
Filtering AF
99.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 98.9%
Overall
94.6%
1,527,369/1,614,020 alleles · common
exomes 1,395,117/1,461,798 · genomes 132,252/152,222 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 100% | 1 |
| European (non-Finnish) | 96.3% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 96.2% | 1 |
| Amishnot grpmax-eligible | 95.6% | 1 |
| Finnishnot grpmax-eligible | 95.5% | 1 |
| Admixed American | 95.4% | 1 |
| South Asian | 95.1% | 1 |
| Remaining individualsnot grpmax-eligible | 94% | 1 |
| Middle Eastern | 93.1% | 1 |
| African / African-American | 63.3% | 2 |
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
- NAT10
- Protein
- p.Pro562=
- Coding
- c.1686C>T
- MANE Select
- NM_024662
- dbSNP
- rs2957518
- Type
- single nucleotide variant
- Location
- chr11:34133094 (GRCh38)
- Gene constraint
- LOEUF 0.935 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.61 · 4 PDB
- Residue 562
- the n-acetyltransferase domain
Similar variants
- NAT10 p.Asn132Asp Uncertain significance ★★ ⚠ same type
- NAT10 c.2885+6G>C Benign ★★ same type
- NAT10 c.373-7C>T Benign ★★ same type
- NAT10 p.Ala983Thr Benign ★★ same type
- NAT10 p.Gln203= Benign ★★ same type
- NAT10 p.Pro224Leu Benign ★★ same type
- NAT10 p.Thr153= Benign ★★ same type
- NAT10 p.Thr929Met 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/nat10-p-pro562 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown