Main Analysis Area

Data Attributes

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

Associated Samples

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

Evidence

  • 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).

Frequency

  • 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)

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