NOS2 p.Thr99=
c.297A>T · rs28730832 · VCV782899
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.98%, eas)
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 -8.7 | GERP -3.7 |
| Overall | ||
| CADD | 0.558 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.98%
East Asian · 1,786/44,882 alleles
Filtering AF
3.83%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.76%
Overall
0.127%
2,052/1,614,144 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 3.98% | 25 |
| Remaining individualsnot grpmax-eligible | 0.266% | 376 |
| African / African-American | 0.104% | 962 |
| South Asian | 0.0121% | 8,279 |
| Admixed American | 0.00666% | 15,005 |
| European (non-Finnish) | 0.000593% | 168,573 |
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
- NOS2
- Protein
- p.Thr99=
- Coding
- c.297A>T
- MANE Select
- NM_001029861 · reported on NM_000625
- dbSNP
- rs28730832
- Type
- single nucleotide variant
- Location
- chr17:27788830 (GRCh38)
- Structure
- AlphaFold pLDDT 76.58
Similar variants
- NOS2 c.1005-10T>C Benign ★★ same type
- NOS2 p.Arg1018Ser Likely benign ★★ same type
- NOS2 p.Glu1111= Benign/Likely benign ★★ same type
- NOS2 p.Gly360= Likely benign ★★ same type
- NOS2 p.Phe319= Benign ★★ same type
- NOS2 p.Val1110= Benign ★★ same type
- NANOS2 p.Ala52Glu Uncertain significance ★ ⚠ same type
- NANOS2 p.Ala52Val 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/nos2-p-thr99 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown