NOS2 p.Val39=
c.117G>A · rs200895544 · VCV759872
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.016%, 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 -0.023 | GERP -0.66, phastCons 0.001 |
| Overall | ||
| CADD | 4.065 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.016%
African / African-American · 12/74,902 alleles
Filtering AF
0.00922%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00722%
Overall
0.000868%
14/1,613,470 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.016% | 6,242 |
| Admixed American | 0.00167% | 59,996 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,476 |
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.Val39=
- Coding
- c.117G>A
- MANE Select
- NM_001029861 · reported on NM_000625
- dbSNP
- rs200895544
- Type
- single nucleotide variant
- Location
- chr17:27789682 (GRCh38)
- Structure
- AlphaFold pLDDT 76.58
- Residue 39
- the 'disordered' region
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-val39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown