NOS1 p.Ser153=
c.459G>A · rs372921010 · VCV799875
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0427%, 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 -20 | GERP -4.2 |
| Overall | ||
| CADD | 0.024 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0427%
African / African-American · 32/74,994 alleles
Filtering AF
0.031%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0271%
Overall
0.00292%
47/1,611,426 alleles · ultra-rare
exomes 24/1,459,146 · genomes 23/152,280 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0427% | 2,344 |
| South Asian | 0.0066% | 15,154 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,595 |
| East Asian | 0.00223% | 44,798 |
| European (non-Finnish) | 0.000339% | 294,634 |
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.Ser153=
- Coding
- c.459G>A
- MANE Select
- NM_000620
- dbSNP
- rs372921010
- Type
- single nucleotide variant
- Location
- chr12:117330611 (GRCh38)
- Structure
- AlphaFold pLDDT 61.90 · 1 PDB
Similar variants
- NOS1 p.Ser153Leu Benign ★★ same residue
- 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
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-ser153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown