SNPnexus - Human Variant Annotation Tool
SNPnexus was first released in November 2008 with the objective of bridging the gap between researchers and the vast volume of genomic data generated by high-throughput technologies. Since its inception, SNPnexus has served as a premier resource for functional variant annotation, assisting the scientific community in assessing the potential significance of sequence variations and prioritizing phenotypically impactful candidates for downstream experimentation.
Over the years, SNPnexus has undergone four major upgrades, each improving performance, adding new annotations, and introducing novel capabilities driven by the needs of our global user community. Today, SNPnexus is a widely adopted platform, cited extensively in genomic research and supported by a steadily growing user base.
The 2025 Release: Version 5
For this latest release, SNPnexus has undergone a complete redesign of both its internal architecture and user interface. Key enhancements include:
- Performance Optimisation: A complete overhaul of the internal engine to ensure better stability, faster processing and future scalability.
- Multi-Sample Queries: A high-priority feature allowing the simultaneous analysis of up to six files to facilitate longitudinal studies and cohort comparisons.
- Advanced Pre-Filtering: New capabilities to focus analysis on specific genomic subsections (e.g., chromosomal regions, gene lists, or exonic mutations) prior to processing.
- Optional User Registration: An optional account system to help researchers track and manage their historical queries.
Accessibility and Licensing
SNPnexus is freely available for academic and non-profit use. The majority of our integrated datasets are also free for academic and non-profit purposes.
Commercial Use: Please contact the relevant data sources directly for information regarding licensing for commercial purposes. For inquiries regarding a customized or commercial version of the platform, please contact us at info@snp-nexus.org.
Annotation Integrity & Data Sources
SNPnexus aggregates data provided by external, independent tools and resources to produce comprehensive reports. We advise users to exercise professional discretion when interpreting findings. If necessary, please consult the individual primary resources and related peer-reviewed publications to verify the data provided.
SNPnexus support the Human Reference Assemblies GRCh37 (hg19) and GRCh38 (hg38). The table below describes the primary data sources and versions utilised in this release:
| Category | GRCh37/hg19 | GRCh38/hg38 | Licensing | |||
|---|---|---|---|---|---|---|
| Source | Updated | Source | Updated | |||
| Genomic Mapping and dbSNP database | UCSC hg19, Ensembl v111, dbSNP 156 | UCSC hg38, Ensembl v115, dbSNP 156 | - | |||
| Genomic Consequence | Ensembl | Ensembl 111 | Jan 2024 | Ensembl 115 | Sep 2025 | - |
| NCBI RefSeq | UCSC hg19 | Sep 2024 | UCSC hg38 | Aug 2025 | - | |
| CCDS | NCBI | Oct 2022 | NCBI | Oct 2022 | - | |
| In-Silico Prediction for Coding Mutations | SIFT | Ensembl 112 | May 2024 | Ensembl 115 | Sep 2025 | - |
| PolyPhen | Ensembl 112 | May 2024 | Ensembl 115 | Sep 2025 | - | |
| REVEL | Revel v1.3 | May 2021 | Revel v1.3 | May 2021 | Non-Commercial Use | |
| AlphaMissense | AlphaMissense v3 | Sep 2023 | AlphaMissense v3 | Sep 2023 | Non-Commercial Use | |
| CADD | CADD v.1.7 | Feb 2024 | CADD v.1.7 | Jan 2024 | Non-Commercial Use | |
| In-Silico Prediction for Non-Coding Mutations | CADD | CADD v1.7 | Feb 2024 | CADD v1.7 | Jan 2024 | Non-Commercial Use |
| ReMM | ReMM v0.4 | 2023 | ReMM v0.4 | 2023 | Contact Authors | |
| JARVIS | JARVIS v1 (UCSC) | Mar 2022 | JARVIS v1 (UCSC) | Mar 2022 | Contact Authors | |
| Population Frequency Data | 1000 Genomes Project | Ensembl | Jan 2024 | Ensembl 115 | Sep 2025 | - |
| Allele Frequency Aggregator (ALFA) | ALFA v4 (NCBI) | Apr 2025 | ALFA v4 (NCBI) | Apr 2025 | - | |
| Genome Aggregation Database (gnomAD) | gnomAD 4.1 (Ensembl) | Sep 2024 | gnomAD 4.1 (Ensembl 115) | Sep 2025 | - | |
| Conserved Regions | Phast (100 vertebrates conserved elements score) | UCSC | Apr 2014 | UCSC | Sep 2015 | - |
| GERP++ (92 mammals conservation score) | GERP | May 2011 | Ensembl 115 | Jun 2025 | - | |
| Biological Context | Reactome Pathways | Reactome.org | V95 (Dec 2025) | Reactome.org | V95 (Dec 2025) | - |
| KEGG Pathways | Kegg.jp | Dec 2025 | Kegg.jp | Dec 2025 | Academic use only. Contact Authors | |
| Genotype/Tissue Expression (GTEx) | GTEx Portal | V10 | GTEx Portal | V10 | - | |
| Phenotype/Trait Association | ClinVar | ClinVar (NCBI) | 1st Feb 2026 | ClinVar (NCBI) | 1st Feb 2026 | - |
| GWAS Catalog | GWAS Catalog (UCSC) | Nov 2025 | GWAS Catalog (EBI) | Nov 2025 | - | |
| COSMIC | COSMIC v103 | Nov 2025 | COSMIC v103 | Nov 2025 | Only Academic Use. Contact Authors | |
How to Cite SNPnexus
If you use SNPnexus in your research, please cite the following publication:
-
Jorge Oscanoa, Lavanya Sivapalan, Emanuela Gadaleta, Abu Z Dayem Ullah, Nicholas R Lemoine, Claude Chelala
SNPnexus: a web server for functional annotation of novel and existing cancer variants. Nucleic Acids Research, Volume 48, Issue W1, 2020, Pages W185–W192.