Table 1.
Summary of SNPnexus features present in the current version
| Feature | SNPnexus v4 | |
|---|---|---|
| Input queries | Human assembly | GRCh37 / GRCh38 |
| Variation format | Genomic coordinates (known/unknown) | |
| Chromosomal region (known) | ||
| dbSNP rs# (known) | ||
| Supported alterations | Single based substitutions, Insertions/deletions (InDel), Block substitutions | |
| Multiple alterations | ||
| IUPAC code supported | ||
| Batch query size | up to 100 000 | |
| Batch query format | VCF or Text file in the SNPnexus variation format (See Supplementary Table S1) | |
| Annotation categories | Gene annotation systems | GRCh37 and GRCh38: Ensembl, RefSeq, UCSC, CCDS |
| GRCh37: Vega, AceView, H-Invitational | ||
| Coding: Synonymous / Nonsynonymous / Stop-gain/loss / Frame-shift / Peptide-shift | ||
| Intronic (splice site) | ||
| Non-coding, 5′/3′-UTR, up/down-stream | ||
| Protein deleterious effects | SIFT (known and novel) and PolyPhen (known) | |
| Population data | gnomAD Exomes: AFR, AMR, EAS, FIN, NFE, OTH, SAS | |
| gnomAD Genomes: AFR, AMR, EAS, FIN, NFE, OTH | ||
| 1000Genomes: AFR, AMR, EAS, EUR, SAS | ||
| HapMap: ASW, CEU, CHB, CHD, GIH, HCB, JPT, LWK, MEX, MKK, TSI, YRI | ||
| Regulatory elements | GRCh37 and GRCh38: miRBASE, CpG islands, TarBase, microRNAs / snoRNAs / scaRNAs, Ensembl Regulatory Build, ENCODE Project, Roadmap Epigenomics | |
| GRCh37: Transcription factor binding sites, Vista enhancers, TargetScan | ||
| Conservation scores | GERP++ scores, PHAST | |
| Disease studies | GRCh37: GAD | |
| GRCh37 and GRCh38: COSMIC, NHGRI-GWAS, ClinVar | ||
| Non-coding scoring | GRCh37: fitCons, EIGEN, FATHMM GWAVA, DeepSEA, ReMM | |
| GRCh37 and GRCh38: CADD, FunSeq2 | ||
| Structural variations | Gain, Loss, Gain+Loss, Duplication, Deletion, Insertion, Complex, Inversion, Tandem duplication, Novel sequence insertion, Mobile element insertion, Sequence alteration | |
| Pathway Analysis | Reactome pathways | |
| Biological / Clinical Interpretation | Cancer genome interpreter | |
| Output | Web format | Html, graphical |
| Filters for query set | Known / Novel variant | |
| Minor allele global frequency | ||
| Genomic consequence | ||
| Predicted protein effect | ||
| In conserved region | ||
| Known phenotype association | ||
| Predicted cancer driver | ||
| Genes involved in query set | ||
| Pathways involved in query set | ||
| Filters per annotation | Filter per dbSNP or Variation ID in each annotation table | |
| Exporting options | Export per annotation or all annotations | |
| Exporting formats | VCF or Tab-delimited texts |