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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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