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Table 3 Logic for variant reporting and validation by Sanger sequencing

From: ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories

Interpretive category

Phenotype applicable

Yes

No (clearly unrelated)

Reportable secondary finding

Uncertain/possibly

No/little phenotypic evidence available

de novo - No/little phenotypic evidence (chose for variants from de novo filter only)

Benign

Do not report

Do not report

Do not report

Do not report

Do not report

Do not report

Likely benign

Report & Sanger

Do not report

Do not report

Report & Sanger

Report

Report & Sanger

Intronic-likely benign

Report & Sanger

Do not report

Do not report

Report & Sanger

Do not report

Do not report

VUS

Report & Sanger

Do not report

Do not report

Report & Sanger

Report

Report & Sanger

Deleterious VUS (only chose for genes with no/little phenotype evidence)

Error - please change category

Error - please change category

Error - please change category

Error - please change category

Report as VUS

Report as VUS & Sanger

Likely pathogenic

Report & Sanger

Need discussion

Report as secondary & Sanger

Report & Sanger

Error - please change to Deleterious VUS

Error - please change to Deleterious VUS

Pathogenic

Report & Sanger

Need discussion

Report as secondary & Sanger

Report & Sanger

Error - please change to Deleterious VUS

Error - please change to Deleterious VUS

Mapping Error

Investigate further via Sanger

Do not report

Do not report

Need discussion

Do not report

Do not report

CompoundHet error

Investigate further via Sanger

Do not report

Need discussion

Need discussion

Do not report

Error - not compound het