At the bottom of the variant table, the clinical cards display complementary information about the variant or the gene.
⚠️ Please note that, when selecting a variant through the check box on the Variant table in VarSome Clinical, the Clinical Cards do not change because the selection of the variant is different from clicking on it to view the variant information. Therefore, to view the clinical cards and the information on a variant, simply click anywhere on the row containing the variant and not the check box to select it for any action.
Variant clinical cards
- General Information: Information about the genomic location of the variant, its type, cytoband, HGVS notation, and sequence.
- Community Contributions: VarSome’s community public contributions for this variant.
- Publications: publications from PubMed related to the selected variant or gene where genes, variants, diseases, phenotypes, chemical compounds, and drugs (if exist) are tagged by our internal AI tool.
⚠️ Please note that we currently only support publications that have a PMID entry.
- Transcripts: Chromosomal location, link to UCSC genome browser, dbSNP (rs number), Refseq transcripts containing the variant, HGVS notation, etc. Available transcripts for the selected genes are displayed (information from RefSeq and Ensembl, along with the MANE transcript). The transcript used in classification is highlighted in the Transcripts summary card.
- Region Browser: Genomic region browser, lollipop graph of the pathogenicity of each variant, frequencies from gnomAD and Bravo, variant visualization with filtering according to databases and coding impact. For further information please refer to section Browsers.
- Sample View: Sample's region browser presents information about SNVs, transcripts, conservation scores/position (and CNVs) of the sample. For further information please refer to section Sample View.
- PharmGKB: Information on the impact of genetic variation on drug response from PharmKGB database.
- Expression Data: Tissue-specific variant expression data from the Genotype-Tissue Expression (GTEx) project.
- GWAS: Associations of specific genetic variations with particular diseases from the genome-wide association study (GWAS) database.
- ACMG Classification: The ACMG Classification and its triggered rules for the selected variant.
- ClinVar: Information about clinical associated phenotypes connected to the selected variant. Description/Submitter column displays ClinVar Comments.
- Frequencies: If known, Gnomad frequencies for the selected variant and for any other known variants that overlap with it.
- MitoMap: Information from the Human Mitochondrial Genome Database.
- Conservation Scores: Conservation scores from different resources.
- UniProt Variants: Variant information from UniProt.
- In-Silico Predictors: : Variant pathogenicity predictions produced by in silico predictors. In this clinical card, the pathogenicity is displayed with a different color and there are two bar charts, one for the meta-score (predictor which combines multiple predictors into a single score) and one for the individual predictors.
- ClinGen: Curated data from the ClinGen variants database. Information will be available when the queried variant has already been curated by any of the ClinGen expert panels.
- Structural Variants: A genome browser showing known structural variants in this region.
⚠️ Since some structural variants are very long, the browser will limit the maximum length of variant it displays by default. You can change this parameter to show larger variants by clicking on "Filters" and changing the value of "Max Length".
- Protein Viewer: The 3D protein viewer tool is available to map variants onto the protein structure. By clicking on the “Protein Viewer” card, a new window will open with the 3D Protein Viewer tool. For more information please refer here.
- Nearby Variants (Sample): Variants in the genomic neighborhood of the selected variant. This variant list is not affected by the filters applied to the sample.
- Clinical: ClinVar and Cosmic annotations for the selected variant and for any other known variants that overlap with it.
- Population Frequencies: gnomAD frequencies and coverage, from Gnomad Exomes and Gnomad Genomes.
- #Samples: The number of samples in which a specific variant has been found. This column gets updated daily. The number of homozygotes and heterozygotes in Saphetor for the variants are shown, but only sample IDs of samples analyzed by you and your group are reported. See more here: Sample cross-referencing.
- OMIM: Information about phenotypes related to the selected variant, as retrieved from Online Mendelian Inheritance in Man®.
- LOVD: Presents the clinical evidence available from the Leiden Open Variation Database (LOVD) for a given variant and it has also been incorporated into the Germline Classification as a new source of clinical evidence.
- DVD: Variant annotations from the Deafness Variation Database. DVD provides a comprehensive guide to genetic variation in genes known to be associated with deafness.
- Multi: Displays the components and their corresponding files used to run the multi-sample analysis, and if these have been selected as affected or not.
- Audit trail: This shows the record of the actions that have been made by all users of a group on the samples analyzed. Only the group supervisor has access to this information.
Additional cards for somatic samples:
- AMP Classification: The AMP tier and the set of triggered rules for the selected variant.
- JAX CKB: Somatic gene variant annotations and related content provided by The Jackson Laboratory Clinical Knowledgebase.
- CiViC: Somatic variant annotations retrieved from CiViC.
- PMKB: Clinical interpretations of somatic variants retrieved from PMKB.
- Cancer Samples Summary: Aggregated information across different data sources.
- Cosmic: Somatic variant annotations from COSMIC database.
- ICGC Somatic: Somatic variant annotations from ICGC database.
- Cancer Hotspots: Somatic annotations from Cancer Hotspots database.
- GDC: Somatic variant annotations from GDC database.
- cBioPortal: Summary of samples matched in cBioPortal with the selected somatic variant.
- IARC TP53 Somatic & Germline: Somatic annotations of TP53 gene mutations in human cancers.
- DoCM: Information retrieved from DoCM, about known, disease-causing mutations associated with the variant.
Gene clinical cards
- Gene basic info: Description, synonyms, cytoband, links to clinical or other resources.
- Transcripts: Strand, chromosomal location, length, mRNA length, UniProt accession number, etc.
- Publications: Publications from PubMed related to the selected gene where genes, variants, diseases, phenotypes, chemical compounds, drugs (if exist) are tagged by our internal AI tool.
- Gene function: Functions related to the selected gene, as provided by Genetics Home Reference (GHR).
- Known gene variants: Variants in the selected gene with known pathogenicity.
- dbSNFP: Functional prediction and annotation of all potential non-synonymous single-nucleotide variants.
- GnomAD Genes: Data summary from a wide variety of large-scale sequencing projects associated with the selected gene.
- EBI Gene2Phenotype: Gene association with a disease entity based on an allelic requirement and a mutational consequence.
- GenCC: Curated information about the gene-disease relationship.
- NHI ClinGen Disease Validity: Gene-disease association validity information.
- DOMINO: Probability of the selected gene to cause dominant changes.
- PanelApp gene lists: Catalog of available gene panels including the selected gene.
- Clinical Genomic Database: Age affected, condition, inheritance, indicated intervention categories, publications as retrieved from Clinical Genomic Database.
- Human Phenotype Ontology: Disease and their phenotypic abnormalities associated with the selected gene.
- Human Protein Atlas: Protein expression information by cell and tissue type
- Fusion GDB: Functional annotation of fusion genes in cancer and their related drugs
- Gene Expression: Tissue-specific gene expression data from the Genotype-Tissue Expression (GTEx) project.
- Protein Viewer: The 3D protein viewer tool is available to map variants onto the selected protein structure. By clicking on the “Protein Viewer” card, a new window will open with the 3D Protein Viewer tool. For more information please refer to here.
- JAX CKB: Evidence and clinical trials content related to the selected gene as provided by The Jackson Laboratory Clinical Knowledge base.
- OMIM: Information about phenotypes related to the selected gene, as retrieved from the Online Mendelian Inheritance in Man®.
- PharmKGB: Information on the impact of genetic variation on drug response from PharmKGB database.
- FDA: Approved drugs associated with the selected gene, from FDA.
- DGI: Information about drug-gene interactions interpreted by the “Drug Gene Interaction” Database.
- CPIC: CPIC levels to genes/drugs retrieved from “Gene Drugs Interactions and Levels”
- AACT Clinical Trials: Information about every clinical study registered in ClinicalTrials.gov associated with the selected gene as provided by AACT.
- Community Contributions: VarSome’s community public contributions for this variant.
Additional cards for somatic samples:
- CiViC: Cancer-related clinical evidence as derived from CiViC database.
- PMKB: Clinical interpretations of gene variants retrieved from PMKB.
- Cancer Gene Census: Information about gene’s mutations that are causally implicated in cancer as retrieved by COSMIC database.
Please note that grayed out tabs are disabled if no related information is available.
Compact view
It is possible to make the clinical cards much smaller by clicking on the “Display Options” wheel on the top right-hand side of the cards panel, and selecting “Compact View”. This removes the summary data from the cards and reduces their size.
