Case quality section

The Case quality section shows the results of individual validation checks and the overall case quality status. Case quality is based on validation of the proband sample.

Use case quality to judge, at a glance, whether a case has enough high-quality, well-annotated variant data to support interpretation.

Case quality checks

Case quality is based on five checks of the proband sample:

• Chromosome validation
• gnomAD validation
• ClinVar validation
• AI Shortlist validation
• mtDNA reference validation

Each check returns one of three results:

• Passed
• Failed
• Skipped — the check does not apply to this case and does not affect case quality.

Note: A chromosome in the proband sample is checked only if it has at least 100 SNVs within the enrichment kit or coding regions. Chromosomes below this threshold are excluded from individual case quality metrics.

Chromosome validation

• Passed: Every checked chromosome has at least one high-quality variant.
• Failed: At least one checked chromosome has no high-quality variants.
• Skipped: The check does not apply to this case.

gnomAD validation

• Passed: Every checked chromosome has at least one gnomAD-annotated variant.
• Failed: At least one checked chromosome has no gnomAD-annotated variants.
• Skipped: The check does not apply to this case.

ClinVar validation

• Passed: Every checked chromosome has at least one ClinVar-annotated variant.
• Failed: At least one checked chromosome has no ClinVar-annotated variants.
• Skipped: The check does not apply to this case.

AI Shortlist validation

• Passed: The AI Shortlist tagged at least one variant.
• Failed: The AI Shortlist tagged no variants.
• Skipped: The gene list has fewer genes than the gene list threshold.

mtDNA reference validation

• Passed: Mitochondrial DNA variants use the rCRS reference.
• Failed: Mitochondrial DNA variants use a different reference.
• Skipped: The case has no mitochondrial DNA data.

Overall case quality status

The overall case quality status appears:

• In the Summary dashboard on the Lab tab.
• Next to the Case quality section title on the Lab tab.
• In the Quality column of the Cases table.

The overall case quality status depends on whether any individual check failed.

• Pass: Every check either passed or was skipped.
• Pass with exceptions (v100.41+) or Fail (v100.40 and earlier): At least one check failed.