Variant Prediction

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Variant Prediction

We use SnpEff to perform variant prediction. Variants are labeled as having a LOW, MODERATE, or HIGH impact based on the location and nature of the variant. We do not include MODIFIER annotations provided by SnpEff. Variant impacts are detailed within The Sequence Ontology Project.

Putative Effect Sequence Ontology Term
HIGH chromosome_number_variation
HIGH exon_loss_variant
HIGH frameshift_variant
HIGH rare_amino_acid_variant
HIGH splice_acceptor_variant
HIGH splice_donor_variant
HIGH start_lost
HIGH stop_gained
HIGH stop_lost
HIGH transcript_ablation
MODERATE 3_prime_UTR_truncation+exon_loss
MODERATE 5_prime_UTR_truncation+exon_loss
MODERATE coding_sequence_variant
MODERATE disruptive_inframe_deletion
MODERATE disruptive_inframe_insertion
MODERATE inframe_deletion
MODERATE inframe_insertion
MODERATE missense_variant
MODERATE regulatory_region_ablation
MODERATE splice_region_variant
MODERATE TFBS_ablation
LOW 5_prime_UTR_premature
LOW initiator_codon_variant
LOW splice_region_variant
LOW start_retained
LOW stop_retained_variant
LOW synonymous_variant



1.1.0