NOS1 p.Ser1016=
c.3048A>C · rs370076270 · VCV2643375
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00136%, nfe)
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 -8.5 | GERP -4.4 |
| Overall | ||
| CADD | 0.191 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00136%
European (non-Finnish) · 16/1,175,066 alleles
Filtering AF
0.000806%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000652%
Overall
0.00106%
17/1,607,464 alleles · very rare
exomes 12/1,455,378 · genomes 5/152,086 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00136% | 73,441 |
| African / African-American | 0.00134% | 74,774 |
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.Ser1016=
- Coding
- c.3048A>C
- MANE Select
- NM_000620
- dbSNP
- rs370076270
- Type
- single nucleotide variant
- Location
- chr12:117234752 (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-ser1016 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown