3.7.3. Project Options

When starting a VSClinical workflow, you will be greeted by the VSClinical Project Options dialog, which allows you to configure your workflow. These options are grouped into five tabs:

  • Options: The first tab allows you to select the database catalogs used by VSClinical to store interpretation data. The variant catalog stores interpretation information about classified variants, the CNV catalog stores information about classified CNVs, and the gene dosage sensitivity catalog stores evidence supporting or refuting each gene’s haploinsufficiency or triplosensitivity. See Assessment Catalog View for more information on assessment catalogs.

  • ACMG Consortium Sources: The second tab is used to specify consortium sources. These sources contain previously classified variants and are used to determine if a variant has been previously classified as pathogenic or benign.

  • ACMG Previously Interpreted Variant Sources: The third tab is used to specify previously interpreted variant sources. These sources contain expert curated variant interpretations along with classifications, applicable criteria, and associated comments. Variant’s in these sources will be automatically classified and assigned criteria based on the associated interpretation in the source database.

  • ACMG Frequency Sources: The fourth tab is used to specify population frequency sources. These sources provide the variant-level allele frequencies used for recommending the criteria BA1, BS1, and PM2. If these sources include sub-population fields, then the sub-population with the largest allele frequency meeting the minimum allele count will be used for the recommendation of criteria.

  • ACMG Control Sources: The final tab is used to specify control sources. These sources are assumed to contain only healthy adult individuals and are used to recommend the BS2 criterion.

VSClinical Options