Databases versions
Check the version of the databases used on the SeqOne platform
💡 This list was last updated for platform version Spring 2026 🌸 released on April 29th, 2026.
The various databases and versions used by the SeqOne tools and worksets are described in the tables below.
When a database is not specifically associated with a genome version, the matching column displays N/A.
Variant annotation databases
| Name | Version | Genome | Description |
|---|---|---|---|
| VEP cache (RefSeq) | 112 | GRCh37, GRCh38 | Ensembl Variant Effect Predictor cache using RefSeq transcripts |
| Valid for the following workset versions: | |||
| • GermlineVar, GermlineFamily, SomaVar, SomaVar LF and SomaRNA versions ≥ 2.0 | |||
| • GermVar Tertiary and GermVar Tertiary Family versions ≥ 1.8 | |||
| • SomaCGP version ≥ 0.6 | |||
| VEP cache (RefSeq) | 107 | GRCh37, GRCh38 | Ensembl Variant Effect Predictor cache using Ensembl transcripts |
| Valid for the following workset versions: | |||
| • GermlineVar, GermlineFamily, SomaVar, SomaVar LF and SomaRNA versions ≤ 2.0 | |||
| • GermVar Tertiary and GermVar Tertiary Family versions ≤ 1.8 | |||
| • SomaCGP version ≤ 0.6 | |||
| VEP cache (Ensembl) | 112 | GRCh37, GRCh38 | Ensembl Variant Effect Predictor cache using Ensembl transcripts |
| Valid for the following workset versions: | |||
| • GermlineVar, GermlineFamily, SomaVar, SomaVar LF and SomaRNA versions ≥ 2.0 | |||
| • GermVar Tertiary and GermVar Tertiary Family versions ≥ 1.8 | |||
| • SomaCGP version ≥ 0.6 | |||
| VEP cache (Ensembl) | 107 | GRCh37, GRCh38 | Cache Ensembl Variant Effect Predictor using Ensembl transcripts |
| Valid for the following workset versions: | |||
| • GermlineVar, GermlineFamily, SomaVar, SomaVar LF and SomaRNA versions ≤ 2.0 | |||
| • GermVar Tertiary and GermVar Tertiary Family versions ≤ 1.8 | |||
| • SomaCGP version ≤ 0.6 | |||
| dbNSFP | 4.3a | GRCh37, GRCh38 | Database of human non-synonymous SNPs and their functional predictions |
| dbscSNV | 1.1 | GRCh37, GRCh38 | Database for predicting splicing changes caused by variants |
| ClinVar | 2026-02 | GRCh37, GRCh38 | Database of clinically relevant variants |
| COSMIC coding mutations | v103 | GRCh37, GRCh38 | Catalogue of Somatic Mutations in Cancer |
| dbSNP | 180423 (GRCh37), 180418 (GRCh38) | GRCh37, GRCh38 | Database of single nucleotide polymorphisms |
| gnomAD | 4.1.0, | ||
| 2.1 | GRCh37, GRCh38 | Genome Aggregation Database, large-scale exome and genome sequencing project | |
| 1000 Genomes | 130502 (GRCh37), 161214 (GRCh38) | GRCh37, GRCh38 | A deep catalog of human genetic variation |
| LOVD | 190531 | GRCh37 | Leiden Open Variation Database, gene-centered collection of variants |
| SpliceAI | 20230210 | GRCh37, GRCh38 | Deep learning-based tool to identify splice variants |
| DECIPHER | 3 | GRCh37, GRCh38 | DECIPHER (DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources) Haploinsufficiency Predictions |
| ClinGen | 240808 | GRCh37, GRCh38 | NIH central resource that defines the clinical relevance of genes and variants for use in precision medicine and research. |
| IARC TP53 | R21 - Jan, 2025 | GRCh37, GRCh38 | Detailed TP53 variant database. |
Genes and transcripts databases
| Name | Version | Genome | Description |
|---|---|---|---|
| RefSeq canonical transcripts | 220307_2023-10 (GRCh37), 20211119_2024-03 (GRCh38) | GRCh37, GRCh38 | Canonical transcripts from NCBI RefSeq database |
| RefGene sorted | 220307_2023-10 (GRCh37), 20211119_2024-03 (GRCh38) | GRCh37, GRCh38 | Sorted gene annotations from NCBI RefSeq |
| RefSeq GFF | 220307 (GRCh37), 20211119 (GRCh38) | GRCh37, GRCh38 | Gene Feature Format file from NCBI RefSeq |
| MANE | v1.4 | GRCh37, GRCh38 | Matched Annotation from NCBI and EMBL-EBI (MANE) |
Functional prediction and conservation databases
| Name | Version | Genome | Description |
|---|---|---|---|
| MaxEntScan | 040420 | N/A | Maximum Entropy Model for Splice Site Prediction |
| GeneSplicer | 090910 | N/A | Splice site prediction tool |
| ACMG-ML ClinVar | 240821 (GRCh37), 240822 (GRCh38) | GRCh37, GRCh38 | Machine learning-based ACMG classification using ClinVar data |
Databases on repeated sequences and structural variants
| Name | Version | Genome | Description |
|---|---|---|---|
| RepeatMasker (rmsk) | 190909 (GRCh37), 210903 (GRCh38) | GRCh37, GRCh38 | Database of repetitive elements in the genome |
| Dfam | 3.0 | N/A | Database of repetitive DNA families |
Databases on diseases and phenotypes
| Name | Version | Genome | Description |
|---|---|---|---|
| OMIM | 20 March 2026 | ||
| N/A | Online Mendelian Inheritance in Man, catalog of human genes and genetic disorders | ||
| Diseases to Genes | 230331 | N/A | Mapping of diseases to associated genes |
| HPO | 2024-04-26 | N/A | Human Phenotype Ontology |
| Disease Ontology | 2023-07 | N/A | Standardized ontology for human disease |
| PhenoGenius model | v3.1 | N/A | Machine learning model for phenotype analysis |
| PanelApp Australia/England | 20 March 2026 | ||
| N/A | Database of gene panels associated to diseases |
Cancer-specific databases
| Name | Version | Genome | Description |
|---|---|---|---|
| COSMIC Fusion | v102 | GRCh37, GRCh38 | Catalogue of Somatic Mutations in Cancer - Gene fusions |
| COSMIC Mutation Census | v103 | GRCh37, GRCh38 | Catalogue of Somatic Mutations in Cancer - Mutation census |
| CIViC | 171201 | N/A | Clinical Interpretation of Variants in Cancer |
| Cancer Gene Role | 220822 | N/A | Database of cancer gene roles |
| JAX-CKB | 2026-02 | N/A | Jackson Laboratory Clinical Knowledgebase for cancer |
| TCGA | 202102 | GRCh37 | The Cancer Genome Atlas (TCGA) - Variants |
Other specialized databases
| Name | Version | Genome | Description |
|---|---|---|---|
| GFF Protein Domains (pfam) | 180306 (GRCh37), 240320 (GRCh38) | GRCh37, GRCh38 | Gene Feature Format file for protein domains |
| FLT3 exons 13 to 15 | 240311 | GRCh37, GRCh38 | Specific exons of the FLT3 gene |
| Cytobands | 180223 (GRCh37), | ||
| 221206 (GRCh38) | GRCh37, GRCh38 | Chromosome band information | |
| HGNC Genes | 220926 | N/A | HUGO Gene Nomenclature Committee standardized gene names |
| STRchive | **v2.16.0 | ||
| (74 loci)** | N/A | An archive of STRs associated with human diseases.https://strchive.org/loci |