BaseSpace Variant Interpreter FAQs

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  • Workflow


  • BaseSpace Variant Interpreter uses the following annotation sources: dbSNP, Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, 1000 Genomes, Exome Variant Server (EVS), Exome Aggregation Consortium (ExAC), PolyPhen, and SIFT.

    No, BaseSpace Variant Interpreter does not currently support direct comparison of analysis results from two different samples.

    No. The software uses the following default classification schemes for tumor and germline samples:

    • Somatic analysis—FDA guidance available, general guidance available, inclusion criteria for clinical trial, and other reportable variant.
    • Germline analysis—Pathogenic, Likely Pathogenic, Variant of Unknown Significance (VUS), Likely Benign, and Benign. These categories follow ACMG guidelines.

    No. For germline variants, the software uses a simple rule set to predict the classification:

    • Variants are automatically ranked and prioritized based on their annotations, predicted consequence (loss of function, missense, or noncoding) and population allele frequency (using the highest frequency from ExAC, 1000 Genomes, and EVS).
    • Variants are typically assigned the ClinVar pathogenicity unless the variant is greater than 5% population frequency, in which case they are assigned Benign per ACMG guidelines.
    • Variants without ClinVar entries that are common (over 1% population frequency) are assigned Likely Benign.
    • Variants without ClinVar entries that are uncommon (less than 1% population allele frequency) are assigned Likely Pathogenic if loss-of-function (frameshift, stop-gained or essential splice), VUS if a missense or near-splice, and Likely Benign if noncoding.

    This pathogenicity autoscoring is only a suggestion. Review these predictions, the provided annotations, and all evidence for the variant before assigning your final interpretation.

    When both alleles of a heterozygous position are different from the reference, as in a tri-allelic position, the variants are split into 2 lines and both variants are annotated.

    No. BaseSpace Variant Interpreter does not support comparisons of two or more groups of samples. Use BaseSpace Cohort Analyzer for cohort or population analysis.