# OneKGPd annotation vocabularies
Controlled-vocabulary terms accepted by the CSV annotation-filter flags of
`onekgpd_api.py`. Values are **case-insensitive** and resolved by exact member
name; pass them as comma-separated lists (e.g.
`--consequence MISSENSE_VARIANT,STOP_GAINED`). Multiple values within one flag
are combined with **OR**; different flags combine with **AND**.
> These lists are the complete set of valid tokens for each flag. A value not
> in the relevant list is rejected with an error listing the valid values.

## Consequence (SO consequence terms) — `--consequence`
41 terms:
- `TRANSCRIPT_ABLATION`
- `SPLICE_ACCEPTOR_VARIANT`
- `SPLICE_DONOR_VARIANT`
- `STOP_GAINED`
- `FRAMESHIFT_VARIANT`
- `STOP_LOST`
- `START_LOST`
- `TRANSCRIPT_AMPLIFICATION`
- `INFRAME_INSERTION`
- `INFRAME_DELETION`
- `MISSENSE_VARIANT`
- `PROTEIN_ALTERING_VARIANT`
- `SPLICE_REGION_VARIANT`
- `INCOMPLETE_TERMINAL_CODON_VARIANT`
- `START_RETAINED_VARIANT`
- `STOP_RETAINED_VARIANT`
- `SYNONYMOUS_VARIANT`
- `CODING_SEQUENCE_VARIANT`
- `MATURE_MIRNA_VARIANT`
- `FIVE_PRIME_UTR_VARIANT`
- `THREE_PRIME_UTR_VARIANT`
- `NON_CODING_TRANSCRIPT_EXON_VARIANT`
- `INTRON_VARIANT`
- `NMD_TRANSCRIPT_VARIANT`
- `NON_CODING_TRANSCRIPT_VARIANT`
- `UPSTREAM_GENE_VARIANT`
- `DOWNSTREAM_GENE_VARIANT`
- `TFBS_ABLATION`
- `TFBS_AMPLIFICATION`
- `TF_BINDING_SITE_VARIANT`
- `REGULATORY_REGION_ABLATION`
- `REGULATORY_REGION_AMPLIFICATION`
- `FEATURE_ELONGATION`
- `REGULATORY_REGION_VARIANT`
- `FEATURE_TRUNCATION`
- `INTERGENIC_VARIANT`
- `SPLICE_POLYPYRIMIDINE_TRACT_VARIANT`
- `SPLICE_DONOR_5TH_BASE_VARIANT`
- `SPLICE_DONOR_REGION_VARIANT`
- `CODING_TRANSCRIPT_VARIANT`
- `SEQUENCE_VARIANT`

## Impact (VEP impact) — `--impact`
4 terms:
- `HIGH`
- `MODERATE`
- `LOW`
- `MODIFIER`

## VariantType (SO variant class) — `--variant-type`
34 terms:
- `SNV`
- `INSERTION`
- `DELETION`
- `INDEL`
- `SUBSTITUTION`
- `INVERSION`
- `TRANSLOCATION`
- `DUPLICATION`
- `ALU_INSERTION`
- `COMPLEX_STRUCTURAL_ALTERATION`
- `COMPLEX_SUBSTITUTION`
- `COPY_NUMBER_GAIN`
- `COPY_NUMBER_LOSS`
- `COPY_NUMBER_VARIATION`
- `INTERCHROMOSOMAL_BREAKPOINT`
- `INTERCHROMOSOMAL_TRANSLOCATION`
- `INTRACHROMOSOMAL_BREAKPOINT`
- `INTRACHROMOSOMAL_TRANSLOCATION`
- `LOSS_OF_HETEROZYGOSITY`
- `MOBILE_ELEMENT_DELETION`
- `MOBILE_ELEMENT_INSERTION`
- `NOVEL_SEQUENCE_INSERTION`
- `SHORT_TANDEM_REPEAT_VARIATION`
- `TANDEM_DUPLICATION`
- `PROBE`
- `ALU_DELETION`
- `HERV_DELETION`
- `HERV_INSERTION`
- `LINE1_DELETION`
- `LINE1_INSERTION`
- `SVA_DELETION`
- `SVA_INSERTION`
- `COMPLEX_CHROMOSOMAL_REARRANGEMENT`
- `SEQUENCE_ALTERATION`

## FeatureType (VEP feature type) — `--feature-type`
3 terms:
- `TRANSCRIPT`
- `REGULATORYFEATURE`
- `MOTIFFEATURE`

## BioType (VEP biotype) — `--bio-type`
47 terms:
- `PROCESSED_TRANSCRIPT`
- `LNCRNA`
- `ANTISENSE`
- `MACRO_LNCRNA`
- `NON_CODING`
- `RETAINED_INTRON`
- `SENSE_INTRONIC`
- `SENSE_OVERLAPPING`
- `LINCRNA`
- `NCRNA`
- `MIRNA`
- `MISCRNA`
- `PIRNA`
- `RRNA`
- `SIRNA`
- `SNRNA`
- `SNORNA`
- `TRNA`
- `VAULTRNA`
- `PROTEIN_CODING`
- `PSEUDOGENE`
- `IG_PSEUDOGENE`
- `POLYMORPHIC_PSEUDOGENE`
- `PROCESSED_PSEUDOGENE`
- `TRANSCRIBED_PSEUDOGENE`
- `TRANSLATED_PSEUDOGENE`
- `UNITARY_PSEUDOGENE`
- `UNPROCESSED_PSEUDOGENE`
- `READTHROUGH`
- `STOP_CODON_READTHROUGH`
- `TEC`
- `TR_GENE`
- `TR_C_GENE`
- `TR_D_GENE`
- `TR_J_GENE`
- `TR_V_GENE`
- `IG_GENE`
- `IG_C_GENE`
- `IG_D_GENE`
- `IG_J_GENE`
- `IG_V_GENE`
- `NONSENSE_MEDIATED_DECAY`
- `PROMOTER`
- `PROMOTER_FLANKING_REGION`
- `ENHANCER`
- `CTCF_BINDING_SITE`
- `OPEN_CHROMATIN_REGION`

## ClinSignificance (ClinVar significance) — `--clin-significance`
19 terms:
- `CLNSIG_BENIGN`
- `LIKELY_BENIGN`
- `UNCERTAIN_SIGNIFICANCE`
- `LIKELY_PATHOGENIC`
- `PATHOGENIC`
- `DRUG_RESPONSE`
- `ASSOCIATION`
- `RISK_FACTOR`
- `PROTECTIVE`
- `AFFECTS`
- `CONFERS_SENSITIVITY`
- `CONFLICTING_INTERPRETATIONS`
- `NOT_PROVIDED`
- `OTHER`
- `LIKELY_PATHOGENIC_LOW_PENETRANCE`
- `PATHOGENIC_LOW_PENETRANCE`
- `UNCERTAIN_RISK_ALLELE`
- `LIKELY_RISK_ALLELE`
- `ESTABLISHED_RISK_ALLELE`

## AlphaMissense (class) — `--alpha-missense-class`
3 terms:
- `AM_LIKELY_BENIGN`
- `AM_LIKELY_PATHOGENIC`
- `AM_AMBIGUOUS`

## Notes

- ClinVar "benign" is the token `CLNSIG_BENIGN` (note the `CLNSIG_` prefix);
  all other ClinSignificance tokens are the bare term.
- AlphaMissense class is mutually exclusive with the AlphaMissense score bounds
  (`--alpha-missense-score-lt`/`-gt`): set one or the other, not both.
