In BQ to VCF, if the representative_header_file is not provided, the meta-information is inferred from the BigQuery schema. If the variant has annotations, the annotation INFO (something like:
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format:Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|TSL|APPRIS|ENSP|SIFT|PolyPhen|DOMAINS))
is not added in the meta-information.