Skill Tracer
Skills › Scientific Agent Skills › onekgpd › annotation_vocabularies.md

annotation_vocabularies.md

192 lines · skills/onekgpd/references/annotation_vocabularies.md at 5f2bc03

Open on GitHub
1# OneKGPd annotation vocabularies
2Verified against `dnaerys 0.2.1` / protobuf R1.20.0 on 2026-09-30.
3These are the API's accepted enums, not every term in the latest upstream VEP or
4ClinVar vocabulary. A valid enum need not occur in the hosted cohort.
5[Official enum source](https://github.com/dnaerys/dnaerys-python/blob/master/src/dnaerys/_enums.py).
6
7Controlled-vocabulary terms accepted by the CSV annotation-filter flags of
8`onekgpd_api.py`. Values are **case-insensitive** and resolved by exact member
9name; pass them as comma-separated lists (e.g.
10`--consequence MISSENSE_VARIANT,STOP_GAINED`). Multiple values within one flag
11are combined with **OR**; different flags combine with **AND**.
12> These lists are the complete set of valid tokens for each flag. A value not
13> in the relevant list is rejected with an error listing the valid values.

OneKGPd annotation vocabularies

Verified against dnaerys 0.2.1 / protobuf R1.20.0 on 2026-09-30. These are the API's accepted enums, not every term in the latest upstream VEP or ClinVar vocabulary. A valid enum need not occur in the hosted cohort. Official enum source.

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.
Raw lines 1 to 14
15## Consequence (SO consequence terms) — `--consequence`
1641 terms:
17- `TRANSCRIPT_ABLATION`
18- `SPLICE_ACCEPTOR_VARIANT`
19- `SPLICE_DONOR_VARIANT`
20- `STOP_GAINED`
21- `FRAMESHIFT_VARIANT`
22- `STOP_LOST`
23- `START_LOST`
24- `TRANSCRIPT_AMPLIFICATION`
25- `INFRAME_INSERTION`
26- `INFRAME_DELETION`
27- `MISSENSE_VARIANT`
28- `PROTEIN_ALTERING_VARIANT`
29- `SPLICE_REGION_VARIANT`
30- `INCOMPLETE_TERMINAL_CODON_VARIANT`
31- `START_RETAINED_VARIANT`
32- `STOP_RETAINED_VARIANT`
33- `SYNONYMOUS_VARIANT`
34- `CODING_SEQUENCE_VARIANT`
35- `MATURE_MIRNA_VARIANT`
36- `FIVE_PRIME_UTR_VARIANT`
37- `THREE_PRIME_UTR_VARIANT`
38- `NON_CODING_TRANSCRIPT_EXON_VARIANT`
39- `INTRON_VARIANT`
40- `NMD_TRANSCRIPT_VARIANT`
41- `NON_CODING_TRANSCRIPT_VARIANT`
42- `UPSTREAM_GENE_VARIANT`
43- `DOWNSTREAM_GENE_VARIANT`
44- `TFBS_ABLATION`
45- `TFBS_AMPLIFICATION`
46- `TF_BINDING_SITE_VARIANT`
47- `REGULATORY_REGION_ABLATION`
48- `REGULATORY_REGION_AMPLIFICATION`
49- `FEATURE_ELONGATION`
50- `REGULATORY_REGION_VARIANT`
51- `FEATURE_TRUNCATION`
52- `INTERGENIC_VARIANT`
53- `SPLICE_POLYPYRIMIDINE_TRACT_VARIANT`
54- `SPLICE_DONOR_5TH_BASE_VARIANT`
55- `SPLICE_DONOR_REGION_VARIANT`
56- `CODING_TRANSCRIPT_VARIANT`
57- `SEQUENCE_VARIANT`

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
Raw lines 15 to 58
59## Impact (VEP impact) — `--impact`
604 terms:
61- `HIGH`
62- `MODERATE`
63- `LOW`
64- `MODIFIER`

Impact (VEP impact) — --impact

4 terms:

  • HIGH
  • MODERATE
  • LOW
  • MODIFIER
Raw lines 59 to 65
66## VariantType (SO variant class) — `--variant-type`
6734 terms:
68- `SNV`
69- `INSERTION`
70- `DELETION`
71- `INDEL`
72- `SUBSTITUTION`
73- `INVERSION`
74- `TRANSLOCATION`
75- `DUPLICATION`
76- `ALU_INSERTION`
77- `COMPLEX_STRUCTURAL_ALTERATION`
78- `COMPLEX_SUBSTITUTION`
79- `COPY_NUMBER_GAIN`
80- `COPY_NUMBER_LOSS`
81- `COPY_NUMBER_VARIATION`
82- `INTERCHROMOSOMAL_BREAKPOINT`
83- `INTERCHROMOSOMAL_TRANSLOCATION`
84- `INTRACHROMOSOMAL_BREAKPOINT`
85- `INTRACHROMOSOMAL_TRANSLOCATION`
86- `LOSS_OF_HETEROZYGOSITY`
87- `MOBILE_ELEMENT_DELETION`
88- `MOBILE_ELEMENT_INSERTION`
89- `NOVEL_SEQUENCE_INSERTION`
90- `SHORT_TANDEM_REPEAT_VARIATION`
91- `TANDEM_DUPLICATION`
92- `PROBE`
93- `ALU_DELETION`
94- `HERV_DELETION`
95- `HERV_INSERTION`
96- `LINE1_DELETION`
97- `LINE1_INSERTION`
98- `SVA_DELETION`
99- `SVA_INSERTION`
100- `COMPLEX_CHROMOSOMAL_REARRANGEMENT`
101- `SEQUENCE_ALTERATION`

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
Raw lines 66 to 102
103## FeatureType (VEP feature type) — `--feature-type`
1043 terms:
105- `TRANSCRIPT`
106- `REGULATORYFEATURE`
107- `MOTIFFEATURE`

FeatureType (VEP feature type) — --feature-type

3 terms:

  • TRANSCRIPT
  • REGULATORYFEATURE
  • MOTIFFEATURE
Raw lines 103 to 108
109## BioType (VEP biotype) — `--bio-type`
11047 terms:
111- `PROCESSED_TRANSCRIPT`
112- `LNCRNA`
113- `ANTISENSE`
114- `MACRO_LNCRNA`
115- `NON_CODING`
116- `RETAINED_INTRON`
117- `SENSE_INTRONIC`
118- `SENSE_OVERLAPPING`
119- `LINCRNA`
120- `NCRNA`
121- `MIRNA`
122- `MISCRNA`
123- `PIRNA`
124- `RRNA`
125- `SIRNA`
126- `SNRNA`
127- `SNORNA`
128- `TRNA`
129- `VAULTRNA`
130- `PROTEIN_CODING`
131- `PSEUDOGENE`
132- `IG_PSEUDOGENE`
133- `POLYMORPHIC_PSEUDOGENE`
134- `PROCESSED_PSEUDOGENE`
135- `TRANSCRIBED_PSEUDOGENE`
136- `TRANSLATED_PSEUDOGENE`
137- `UNITARY_PSEUDOGENE`
138- `UNPROCESSED_PSEUDOGENE`
139- `READTHROUGH`
140- `STOP_CODON_READTHROUGH`
141- `TEC`
142- `TR_GENE`
143- `TR_C_GENE`
144- `TR_D_GENE`
145- `TR_J_GENE`
146- `TR_V_GENE`
147- `IG_GENE`
148- `IG_C_GENE`
149- `IG_D_GENE`
150- `IG_J_GENE`
151- `IG_V_GENE`
152- `NONSENSE_MEDIATED_DECAY`
153- `PROMOTER`
154- `PROMOTER_FLANKING_REGION`
155- `ENHANCER`
156- `CTCF_BINDING_SITE`
157- `OPEN_CHROMATIN_REGION`

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
Raw lines 109 to 158
159## ClinSignificance (ClinVar significance) — `--clin-significance`
16019 terms:
161- `CLNSIG_BENIGN`
162- `LIKELY_BENIGN`
163- `UNCERTAIN_SIGNIFICANCE`
164- `LIKELY_PATHOGENIC`
165- `PATHOGENIC`
166- `DRUG_RESPONSE`
167- `ASSOCIATION`
168- `RISK_FACTOR`
169- `PROTECTIVE`
170- `AFFECTS`
171- `CONFERS_SENSITIVITY`
172- `CONFLICTING_INTERPRETATIONS`
173- `NOT_PROVIDED`
174- `OTHER`
175- `LIKELY_PATHOGENIC_LOW_PENETRANCE`
176- `PATHOGENIC_LOW_PENETRANCE`
177- `UNCERTAIN_RISK_ALLELE`
178- `LIKELY_RISK_ALLELE`
179- `ESTABLISHED_RISK_ALLELE`

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
Raw lines 159 to 180
181## AlphaMissense (class) — `--alpha-missense-class`
1823 terms:
183- `AM_LIKELY_BENIGN`
184- `AM_LIKELY_PATHOGENIC`
185- `AM_AMBIGUOUS`

AlphaMissense (class) — --alpha-missense-class

3 terms:

  • AM_LIKELY_BENIGN
  • AM_LIKELY_PATHOGENIC
  • AM_AMBIGUOUS
Raw lines 181 to 186
187## Notes
189- ClinVar "benign" is the token `CLNSIG_BENIGN` (note the `CLNSIG_` prefix);
190 all other ClinSignificance tokens are the bare term.
191- AlphaMissense class is mutually exclusive with the AlphaMissense score bounds
192 (`--alpha-missense-score-lt`/`-gt`): set one or the other, not both.

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.
Raw lines 187 to 192