Class | Attribute | Value range | Example |
---|---|---|---|
Allele descriptive | Â | Â | Â |
Gene | Gene ID | Internal ID | G0002V5Z |
 | Gene name | HGNC gene symbols | KRAS |
 | Chromosome | 1.. 22, X, Y | 12 |
 | Entrez gene ID | Entrez gene IDs | 3845 |
 | Ensembl gene ID | Ensembl gene IDs | ENSG00000133703 |
 | RefSeq gene ID | RefSeq gene IDs | NG_007524 |
Gene transript | Gene ID | Internal ID | G0002V5Z |
 | Gene transcript ID | Internal ID | T0006OOW |
 | RefSeq transcript ID | RefSeq Transcript IDs | NM_033360 |
 | RefSeq protein ID | RefSeq protein IDs | NP_203524 |
 | Ensemble transcript ID | Ensemble transcript IDs | ENST00000256078 |
 | UniProt ID | UniProt IDs | P01116 |
Gene position | Gene ID | Internal ID | G0002V5Z |
 | Genome version | Genome build IDs | GRCh37.p13 |
 | DNA position | Genomic coordinate | 12p12.1 |
Gene pathway | Gene ID | Internal ID | G0002V5Z |
 | Pathway ID | Internal ID | P003V724 |
Gene pathway | Pathway ID | Internal ID | P003V724 |
 | Common name | Activation of RAS in B cells |  |
 | Kegg ID | Kegg IDs | map04014 |
 | Reactome ID | Reactome IDs | R-HSA-1169092 |
 | PathwayCommons ID | PathwayCommons IDs | R-HSA-1169092 |
Allele interpretive | Â | Â | Â |
Variant | Variant ID | Internal ID | V0000LBB |
 | Variant type | “Single nucleotide variant (SNV)”, “multinucleotide variant (MNV)”, “insertion (INS)”, “deletion (DEL)” | SNV |
Variant position | Variant ID | Internal ID | V0000LBB |
 | Genome version | Genome build IDs | GRCh37.p13 |
 | DNA sub. & position | HGVS genomic coordinate | NC_000012.11:g.25398284C >G |
Gene variant | Gene ID | Internal ID | G0002V5Z |
 | Variant ID | Internal ID | V0000LBB |
 | Variant consequence | “Non-sense”, “missense”, “silent”, “frame shift”, “in-frame”, “3UTR”, “5UTR”, “splice”, “splice-region”, “intronic”, “upstream”, “downstream” | missense |
Gene variant transcript | Gene ID | Internal ID | G0002V5Z |
 | Variant ID | Internal ID | V0000LBB |
 | Gene transcript ID | Internal ID | T0006OOW |
 | Protein sub. & Position | HGVS formatted variants | NM_033360.3(KRAS):c.35G >C (p.Gly12Ala) |
 | Protein domain | Descriptive name of protein domain | Small GTP-binding protein domain |
 | Variant consequence | “Expression”, “amplification”, “deletion”, “fusion”, “loss of function”, “missense” | missense |
 | Risk score | FATHMM, SIFT, PolyPhen | 0.98468, 0, 0.97 |
Somatic interpretive | Â | Â | Â |
Cancer type | Cancer type ID | Internal ID | C000WQFL |
 | Cancer type name | NCI thesaurus | Oncotree IDs | Colorectal cancer |
 | UMLS ID | UMLS concept IDs | C1527249 |
 | HPO ID | HPO concept IDs | HP:0003003 |
Cancer variant | Cancer variant ID | Internal ID | CV00XBQW |
 | Variant ID | Internal ID | V0000LBB |
 | Cancer type ID | Internal ID | C000WQFL |
 | Biomarker class | “Diagnostic”, “prognostic”, “predictive”, “predisposing”, “pharmacogenomic” | predictive |
 | Clinical relevance level() | “Tier 1”, “Tier 2”, “Tier 3” [8] | Tier 2 |
Cancer variant sample | Cancer variant ID | Internal ID | CV00XBQW |
 | Sample ID | Internal ID | SXBQW0A7 |
 | Somatic classification | “Confirmed somatic”, “confirmed germline”, “unknown” | somatic |
 | Allele frequency | Allele frequency in global population | 0.00001647 |
Sample specimen | Sample ID | Internal ID | SXBQW0A7 |
 | Tumor purity | Ratio | 0.763 |
 | TNM status | TNM values | T2N1M1 |
 | Primary / relapse | Primary || relapse | primary |
Cancer variant drug | Cancer variant ID | Internal ID | CV00XBQW |
 | Drug ID | Internal ID | D00000Z9 |
Cancer variant drug effect | Cancer variant ID | Internal ID | CV00XBQW |
 | Drug ID | Internal ID | D00000Z9 |
 | Effect | “Resistant”, “responsive”, “non-responsive”, “sensitive”, “reduced sensitivity”, “other” | Resistance or non-response |
 | Level of evidence | see Table 6 | C |
 | Sublevel of evidence | see Table 6 | 3A |
Drug | Drug ID | Internal ID | D00000Z9 |
 | Substance name | FDA approved | DrugBank substance names | Panitumumab |
 | DrugBank ID | DrugBank IDs | DB01269 |
 | PharmGKB ID | PharmGKB IDs | PA162373091 |
 | FDA ID | FDA IDs | 125147 |
Drug mechanism | Drug ID | Internal ID | D00000Z9 |
 | Molecular mechanism | Description | Binds to the epidermal growth factor receptor (EGFR) on both normal and tumor cells[...] |