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The top section of the variant card shows the annotated gene name, chromosomal position of the variant, rsID (if available) and labels indicating the clinical classification of the variant in ClinVar, Invitae’s internal KB (Invitae) or the lab's KB (KB).
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ClinVar and InvitaeKB variant classifications are annotated based on the chromosomal position, Ref and Alt of the variant, and will show the most severe classification available for that specific variant, irrespective of the gene annotation. |
On the right side of this section, the genotype is displayed as the combination Ref and Alt alleles defined in the VCF. The reference allele is always shown in black and also specifically defined below the genotype presentation, the alternate allele is displayed in red. In the example below, the variant was called in heterozygous state with a C as Ref and an G as Alt, resulting in a 'CG' genotype.
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Scores are highlighted in red if significant as compared to a threshold set in Moon. The threshold in Moon was set based on recommended thresholds in scientific literature. The following thresholds are used as cutoff for highlighting them in the variant card: SIFT <= 0.05; Polyphen > 0.85; MutationTaster > 0.31713; MutationAssessor > 3.5; FATHMM <= -1.5; VEST3 > 0.85; CADD > 15; DANN > 0.85; FATHMM MLK > 0.8; Eigen Phred > 15; GERP > 2; Phylo P > 0; Phastcons > 0.5; SiPhy > 3; EVE > 0.762.
Splice prediction
Two sets of splice predictions scores are annotated in Moon and displayed in the variant cards:
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