Genomic & Genetic Data
- LOCATION - chromosome and genomic coordinate of the variant (link to the UCSC Genome Browser)
- GENE - a popup will show a summary of OMIM disorders and ClinVar entries for the gene including the mode of inheritance when applicable
- REF - the reference allele as presented in the genome reference
- ALT - the alternative call for the main sample
- AA - the amino acid change when applicable
- ZYGOSITY - the genotype call in the main sample
When applicable, a column per associated sample will present an icon depicting the genotype called for the specific variant in the relevant sample (single icon - HET; double icon - HOM).
Clicking on the icon, a table summarizing the variant calling attributes for all the samples in the analysis will be presented.
Variant Calling Q & R
This section includes attributes that can help in assessing the quality and reliability of the genotype call.
- Q&R SCORE- classify calls by their quality (Low: Coverage<10x and GQ<15; Med: Coverage<20x and GQ<50; High: Coverage>=20x and GQ>=50)
- DP4 - read counts (ref+, ref-, alt+, alt-)
- % ALT - the percentage of reads showing the alternative allele
- VARELECT - the score for the association between the gene and the phenotype terms. Clicking on the score will present a summary of the supporting evidence for the association. More details on VarElect HERE
- MATCHED PHENOTYPES - the number of matching terms and the relevant list of phenotypes terms associated with the gene
- COSMIC - list and links to matching COSMIC entries
- CLINVAR - the clinical significance of matching ClinVar entries. A popup will present a summary table of all relevant ClinVar entries with summaries when applicable.
- CIViC - List and links to matching CIViC entries.
Effect & Prediction
- EFFECT - the effect of the variant on the protein level (including splicing effects)
- SEVERITY - classify the effects into three levels:
High: Nonsense, Frameshift, Splicing Sites, Missense (when all prediction tools score as 'Damaging')
Med: Codon indels, Missense (at least one prediction tool scores as 'Damaging')
Low: Synonymous, Splice Site Region, Missense (none of the prediction tools score as 'Damaging')
Expanding this section will present all the prediction tools (GERP, LRT_Pred, PolyPhen2 and SIFT).
- MAX AF - the maximal allele frequency observed in the following control datasets (including a tooltip with the actual count of Het and Hom in ExAC):
1000 Genomes, ESV (~6500 Exomes), ExAC (including GnomAD - ~120,000 Exomes)