Variant Effects¶
This section describes the variant effect names that Jannovar uses for annotating variants. These descriptions are Sequence Ontology (SO) terms and meant to be compatible with the Variant annotations in VCF format standard.
Effect Names¶
The following table gives a list of the used SO terms, the putative impact, and the SO ID. The section Classic Jannovar Effects lists the effect annotations used in the previous Jannovar versions and the corresponding SO-based effect name. The putative impact is one of HIGH, MODERATE, LOW, and MODIFIER. The impact class MODIFIER is both used for terms with hard-to-predict effects and markers (e.g. non_coding_transcript_variant).
| Putative Impact | SO ID | SO Term |
|---|---|---|
| HIGH | SO:1000182 | chromosome_number_variation |
| HIGH | SO:0001624 | transcript_ablation |
| HIGH | SO:0001572 | exon_loss_variant |
| HIGH | SO:0001909 | frameshift_elongation |
| HIGH | SO:0001910 | frameshift_truncation |
| HIGH | SO:0001589 | frameshift_variant |
| HIGH | SO:0001908 | internal_feature_elongation |
| HIGH | SO:0001906 | feature_truncation |
| HIGH | SO:0001583 | mnv |
| HIGH | SO:1000005 | complex_substitution |
| HIGH | SO:0002012 | stop_gained |
| HIGH | SO:0002012 | stop_lost |
| HIGH | SO:0002012 | start_lost |
| HIGH | SO:0001619 | splice_acceptor_variant |
| HIGH | SO:0001575 | splice_donor_variant |
| HIGH | SO:0001619 | rare_amino_acid_variant |
| MODERATE | SO:0001583 | missense_variant |
| MODERATE | SO:0001821 | inframe_insertion |
| MODERATE | SO:0001824 | disruptive_inframe_insertion |
| MODERATE | SO:0001822 | inframe_deletion |
| MODERATE | SO:0001826 | disruptive_inframe_deletion |
| MODERATE | SO:0002013 | 5_prime_utr_truncation |
| MODERATE | SO:0001819 | 3_prime_utr_truncation |
| MODERATE | SO:0001630 | splice_region_variant |
| LOW | SO:0001567 | stop_retained_variant |
| LOW | SO:0001582 | initiator_codon_variant |
| LOW | SO:0001819 | synonymous_variant |
| LOW | SO:0001969 | coding_transcript_intron_variant |
| LOW | SO:0001583 | non_coding_transcript_exon_variant |
| LOW | SO:0001970 | non_coding_transcript_intron_variant |
| LOW | SO:0001983 | 5_prime_UTR_premature_start_codon_gain_variant |
| LOW | SO:0001623 | 5_prime_utr_variant |
| LOW | SO:0001624 | 3_prime_utr_variant |
| MODIFIER | SO:1000039 | direct_tandem_duplication |
| MODIFIER | <custom> | <custom> |
| MODIFIER | SO:0001624 | upstream_gene_variant |
| MODIFIER | SO:0001632 | downstream_gene_variant |
| MODIFIER | SO:0001628 | intergenic_variant |
| MODIFIER | SO:0001819 | tf_binding_site_variant |
| MODIFIER | SO:0001619 | regulatory_region_variant |
| MODIFIER | SO:0002018 | conserved_intron_variant |
| MODIFIER | SO:0001908 | intragenic_variant |
| MODIFIER | SO:0002017 | conserved_intergenic_variant |
| MODIFIER | SO:0001537 | structural_variant |
| MODIFIER | SO:0001580 | coding_sequence_variant |
| MODIFIER | SO:0001908 | intron_variant |
| MODIFIER | SO:0001791 | exon_variant |
| MODIFIER | SO:0001568 | splicing_variant |
| MODIFIER | SO:0001908 | miRNA |
| MODIFIER | SO:0001564 | gene_variant |
| MODIFIER | SO:0001968 | coding_transcript_variant |
| MODIFIER | SO:0001619 | non_coding_transcript_variant |
| MODIFIER | SO:0001624 | transcript_variant |
| MODIFIER | SO:0000605 | intergenic_region |
| MODIFIER | SO:0000340 | chromosome |
| MODIFIER | SO:0001060 | sequence_variant |
Classic Jannovar Effects¶
The original Jannovar used the following terms together with priority levels.
| Priority | Classic Term | Description |
|---|---|---|
| 1 | FS_DELETION | frameshift truncation |
| 1 | FS_DUPLICATION | frameshift duplication |
| 1 | FS_INSERTION | frameshift elongation |
| 1 | FS_SUBSTITUTION | frameshift substitution |
| 1 | MISSENSE | missense |
| 1 | NON_FS_DELETION | inframe deletion |
| 1 | NON_FS_DUPLICATION | inframe duplication |
| 1 | NON_FS_INSERTION | inframe insertion |
| 1 | NON_FS_SUBSTITUTION | inframe substitution |
| 1 | SPLICING | splicing |
| 1 | START_LOSS | startloss |
| 1 | STOPGAIN | stopgain |
| 1 | STOPLOSS | stoploss |
| 1 | SV_DELETION | 1k+ deletion |
| 1 | SV_INSERTION | 1k+ insertion |
| 1 | SV_INVERSION | 1k+ inversion |
| 1 | SV_SUBSTITUTION | 1k+ substitution |
| 2 | ncRNA_EXONIC | ncRNA exonic |
| 2 | ncRNA_SPLICING | ncRNA splicing |
| 3 | UTR3 | UTR3 |
| 4 | UTR5 | UTR5 |
| 5 | SYNONYMOUS | synonymous |
| 6 | INTRONIC | intronic |
| 7 | ncRNA_INTRONIC | ncRNA intronic |
| 8 | DOWNSTREAM | downstream |
| 8 | UPSTREAM | upstream |
| 9 | INTERGENIC | intergenic |
| 10 | ERROR | error |
The following table gives a mapping between classic Jannovar terms to SO-based terms. In some cases, two SO attributes are combined to achieve the same annotation.
| Priority | Classic Term |
|---|---|
| 1 | MISSENSE |
| 1 | FS_DELETION |
| 1 | FS_INSERTION |
| 1 | NON_FS_DELETION |
| 1 | NON_FS_INSERTION |
| 1 | SPLICING |
| 1 | STOPGAIN |
| 1 | STOPLOSS |
| 1 | FS_DUPLICATION |
| 1 | NON_FS_DUPLICATION |
| 1 | FS_SUBSTITUTION |
| 1 | NON_FS_SUBSTITUTION |
| 1 | STARTLOSS |
| 2 | ncRNA_EXONIC |
| 2 | ncRNA_SPLICING |
| 3 | UTR3 |
| 4 | UTR5 |
| 5 | SYNONYMOUS |
| 6 | INTRONIC |
| 7 | ncRNA_INTRONIC |
| 8 | UPSTREAM |
| 8 | DOWNSTREAM |
| 9 | INTERGENIC |
| 10 | ERROR |