The VariantAnnotation record groups different types of annotation records by Variant.
The TranscriptEffect sub record holds information on the effect of a specific allele on a specific transcript. As Variants may overlap multiple transcripts, they may have multiple TranscriptEffect records. Variants with multiple alternate alleles will have multiple TranscriptEffect records per transcript. (2 alternate alleles x 3 transcripts = 6 TranscriptEffect records)
VariantAnnotation records belong to VariantAnnotationSets. VariantAnnotationSets are created by comparing a number of Variants from a VariantSet to a specific set of reference data using specific software tools. A VariantAnnotationSet contains information on reference data and software versions used in calculating the annotation; it is essential this information is exhaustive.