NAT10 p.Asp91=
c.273C>T · rs35401535 · VCV732327
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.132%, 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 0.37 | GERP 1.3, phastCons 0.99 |
| Overall | ||
| CADD | 10.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.132%
African / African-American · 99/75,044 alleles
Filtering AF
0.111%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.103%
Overall
0.00756%
122/1,614,202 alleles · rare
exomes 52/1,461,888 · genomes 70/152,314 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.132% | 758 |
| Middle Eastern | 0.033% | 3,031 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,683 |
| Admixed American | 0.015% | 6,669 |
| South Asian | 0.0011% | 91,072 |
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.Asp91=
- Coding
- c.273C>T
- MANE Select
- NM_024662
- dbSNP
- rs35401535
- Type
- single nucleotide variant
- Location
- chr11:34112124 (GRCh38)
- Gene constraint
- LOEUF 0.935 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.61 · 4 PDB
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.Pro562= Benign ★★ same type
- NAT10 p.Thr153= 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-asp91 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown