In silico predictions filters (v37.0+)
The In silico predictions filters allow filtering variants based on scores from computational prediction tools. These filters help prioritize variants with potential functional or regulatory impact inferred from predictive models.
The filters can operate in a Simple or Advanced mode.
Simple and advanced filtering modes operate independently.
Even with similar settings, results may differ due to variations in filtering logic and options available.
Simple mode
Refine the variant list by setting minimum thresholds for aggregated in silico prediction scores:
Missense prediction (All, Neutral, Damaging)
Conservation (Low, Moderate, High)
Splicing (Low, Moderate, High)
Advanced mode
Fine-tune the variant list by setting minimum thresholds for particular in silico prediction tools:
Missense prediction
REVEL score
Minimum threshold for REVEL missense variant pathogenicity score.
Range: 0-1 using the slider
Custom value: Enter a number within the range in the input field
PrimateAI-3D prediction
PrimateAI-3D missense variant pathogenicity prediction category:
None
Benign
Damaging
CADD Phred score (v38.0+)
Minimum threshold for CADD Phred deleteriousness score. Applicable for SNVs, MNVs, and indels, both coding and non-coding.
Range: 0-99 using the slider
Custom value: Enter a number within the range in the input field
Missense Z-score
Minimum threshold for missense Z-score indicating a gene's intolerance to missense variants.
Range: -8 to 8 using the slider
Custom value: Enter a number within the range in the input field
PLI score
Minimum threshold for PLI score indicating a gene's probability of being intolerant to loss-of-function variants.
Range: 0-1 using the slider
Custom value: Enter a number within the range in the input field
Conservation
GERP RS score
Minimum threshold for GERP RS conservation score.
Range: -12.36 to 6.18 using the slider
Custom value: Enter a number within the range in the input field
Splicing
SpliceAI DS AG score
Minimum threshold for SpliceAI delta scores for splice acceptor site gain.
Range: 0-1 using the slider
Custom value: Enter a number within the range in the input field
SpliceAI DS AL score
Minimum threshold for SpliceAI delta scores for splice acceptor site loss.
Range: 0-1 using the slider
Custom value: Enter a number within the range in the input field
SpliceAI DS DG score
Minimum threshold for SpliceAI delta scores for splice donor site gain.
Range: 0-1 using the slider
Custom value: Enter a number within the range in the input field
SpliceAI DS DL score
Minimum threshold for SpliceAI delta scores for splice donor site loss.
Range: 0-1 using the slider
Custom value: Enter a number within the range in the input field
Default values
When filters are reset to default, the In silico predictions filters are not applied.
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