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Table 1 VEP Impact terms that impact coding gene regions

From: SVAT: Secure outsourcing of variant annotation and genotype aggregation

Term

CDS

Splice

Region

Splice

Acceptor

Splice

Donor

5’

UTR

3’

UTR

Start

Codon

Stop

Codon

Intron

intron_variant

0

0

0

0

0

0

0

0

1

3_prime_UTR_variant

0

0

0

0

0

1

0

0

0

5_prime_UTR_variant

0

0

0

0

1

0

0

0

0

coding_sequence_variant

1

0

0

0

0

0

0

0

0

synonymous_variant

1

0

0

0

0

0

0

0

0

stop_retained_variant

0

0

0

0

0

0

0

1

0

start_retained_variant

0

0

0

0

0

0

1

0

0

incomplete_terminal_codon_variant

1

0

0

0

0

0

0

0

0

splice_region_variant

0

1

0

0

0

0

0

0

0

protein_altering_variant

0

0

0

0

0

0

0

0

0

missense_variant

1

0

0

0

0

0

0

0

0

inframe_deletion

1

0

0

0

0

0

0

0

0

inframe_insertion

1

0

0

0

0

0

0

0

0

transcript_amplification

0

0

0

0

0

0

0

0

0

start_lost

1

0

0

0

0

0

1

0

0

stop_lost

1

0

0

0

0

0

0

1

0

frameshift_variant

1

0

0

0

0

0

0

0

0

stop_gained

0

0

0

0

0

0

0

1

0

splice_donor_variant

0

0

0

1

0

0

0

0

0

splice_acceptor_variant

0

0

1

0

0

0

0

0

0

  1. The first column shows the impact term. Each cell with ‘1’ indicates the gene element that is impacted. The full set of impact terms is provided in Supplementary Table 1 in Additional file 1