NOS1 p.Phe1286=
c.3858C>T · rs372919678 · VCV731444
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00161%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.44 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.15 | GERP -5.4, phastCons 0.039 |
| Overall | ||
| CADD | 12.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00161%
European (non-Finnish) · 19/1,179,956 alleles
Filtering AF
0.00103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00083%
Overall
0.00124%
20/1,613,806 alleles · very rare
exomes 17/1,461,758 · genomes 3/152,048 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00161% | 62,103 |
| African / African-American | 0.00134% | 74,876 |
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
- NOS1
- Protein
- p.Phe1286=
- Coding
- c.3858C>T
- MANE Select
- NM_000620
- dbSNP
- rs372919678
- Type
- single nucleotide variant
- Location
- chr12:117222832 (GRCh38)
- Structure
- AlphaFold pLDDT 61.90 · 1 PDB
Similar variants
- NANOS1 c.-51G>C Benign ★★ same type
- NANOS1 p.Pro34Thr Benign ★★ same type
- NOS1 c.3042-6C>T Benign ★★ same type
- NOS1 p.Ala1337= Likely benign ★★ same type
- NOS1 p.Asp241Asn Benign/Likely benign ★★ same type
- NOS1 p.Asp394Ala Benign/Likely benign ★★ same type
- NOS1 p.Gly595Ser Benign/Likely benign ★★ same type
- NOS1 p.Gly864Asp 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/nos1-p-phe1286 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown