Variant Impact tab

Variant Impact

For each gene, the variant impact is scored based on the severity of the impact of the variant. The heat map is color coded using the following impact score values, where higher values are associated with mutations that have more significant, or worse, impact.

• Unknown: 0

• Synonymous: 1

• Missense: 2

• Non-frameshift block substitution: 3

• Non-frameshift insertion: 4

• Non-frameshift deletion: 4

• Nonsense: 5

• Stop-loss: 6

• Frameshift block substitution: 7

• Frameshift insertion: 7

• Frameshift deletion: 7

• Splice variant: 8

SIFT

A SIFT score predicts whether an amino acid substitution affects protein function. The SIFT score ranges from 0 to 1, where the score of 0 represents the most deleterious amino acid substitution and the score of 1 represents the most tolerated amino acid substitution.

PolyPhen‑2

The PolyPhen‑2 score predicts the possible impact of an amino acid substitution on the structure and function of a human protein. The score represents the probability that a substitution is damaging. The reported score range is 0–2, with the following classifications for the impact of an amino acid substitution.

• Benign: 0–0.99

• Borderline: 1–1.24

• Potentially damaging: 1.25–1.49

• Possibly damaging: 1.5–1.99

• Damaging: ≥2

PhyloP

The PhyloP score measures the evolutionary conservation at individual alignment sites. Positive scores measure conservation, or slower than expected evolution, and represent sites that are predicted to be conserved. Negative scores measure acceleration, or faster than expected evolution, and represent sites that are predicted to be fast-evolving.

Grantham

The Grantham score provides a prediction for the evolutionary distance between the amino acids. A lower score predicts a smaller evolutionary distance. A higher score predicts a greater evolutionary distance.

Gene Order

Select one of following options from the Gene Order dropdown list to arrange the order in which the genes are listed in the heat map.

• Name

• Similarity

• Similarity (left/right reversed)

Sample Order

Select one of following options from the Sample Order dropdown list to arrange the order in which the genes are listed in the heat map.

• Name: Samples are listed alphabetically by name from left to right.

• Similarity: Samples are listed by how similar they are in the fusion calls made, presented from fewest fusions to most fusions from left to right.

• Similarity (left/right reversed): Samples are listed by how similar they are in the fusion calls made, presented from fewest fusions to most fusions from right to left.

• Analysis: Samples are listed alphabetically by analysis name from left to right.

Color Scale

Select a color scale to customize the colors that are displayed in the heat map.

Export Heatmap

You can export and save your heat map in PNG, SVG, and CSV file formats. The file is automatically downloaded once you make your selection from the Export Heatmap dropdown list.