variantreference kind
- Identified by
:variant/idglobal id- Attributes
- 36
- Referenced by
- 1 attributes
Attributes
| Attribute | Type | Cardinality | Description |
|---|---|---|---|
| HGVSc :variant/HGVSc | string | one | The HGVSc string for this variant, see http://varnomen.hgvs.org/ |
| HGVSp :variant/HGVSp | string | many | The HGVSp strings for this variant, see http://varnomen.hgvs.org/ |
| alt-allele :variant/alt-allele | string | one | The alternate allele for this variant |
| alt-allele-2 :variant/alt-allele-2 | string | one | The 2nd alternate allele for this variant |
| alt-amino-acid :variant/alt-amino-acid | string | one | The alternate one letter coded amino acid sequence for this variant (ie A, R) |
| classification :variant/classification | variant.classification | one | The classification of this variant, refers to idents in the 'variant.classification' namespace |
| context :variant/context | string | one | The reference allele per VCF specs, and its five flanking base pairs |
| coordinate-string :variant/coordinate-string | string | one | The coordinate string (summarized genomic coordinate info) for this variant. |
| cosmic :variant/cosmic | string | many | Overlapping COSMIC variants |
| dbSNP :variant/dbSNP | string | many | A list of dbSNP (https://www.ncbi.nlm.nih.gov/projects/SNP/) ids for this variant |
| exac-af :variant/exac-af | string | one | Global allele frequency from ExAC, in range [0, 1]. See http://exac.broadinstitute.org/ |
| exac-af-adj :variant/exac-af-adj | float | one | Adjusted global allele frequency from ExAC, in range [0, 1]. See http://exac.broadinstitute.org/ |
| exac-afr :variant/exac-afr | float | one | African/African-American allele frequency from ExAC, in range [0, 1]. See http://exac.broadinstitute.org/ |
| exac-amr :variant/exac-amr | float | one | American allele frequency from ExAC, in range [0, 1]. See http://exac.broadinstitute.org/ |
| exac-eas :variant/exac-eas | float | one | East Asian allele frequency from ExAC, in range [0, 1]. See http://exac.broadinstitute.org/ |
| exac-fin :variant/exac-fin | float | one | Finnish allele frequency from ExAC, in range [0, 1]. See http://exac.broadinstitute.org/ |
| exac-nfe :variant/exac-nfe | float | one | Non-Finnish European allele frequency from ExAC, in range [0, 1]. See http://exac.broadinstitute.org/ |
| exac-oth :variant/exac-oth | float | one | Other allele frequency from ExAC, in range [0, 1]. See http://exac.broadinstitute.org/ |
| exac-sas :variant/exac-sas | float | one | South Asian allele frequency from ExAC, in range [0, 1]. See http://exac.broadinstitute.org/ |
| external-ids :variant/external-ids | string | many | A list of IDs which may appear in external databases, e.g. rs*, COS*, agnostic to a specific reference. Do not use this attribute if the identifier is not prefixed or its reference source is not otherwise discernible. |
| feature-type :variant/feature-type | variant.feature | one | The type of feature (transcript, regulatory, motif), refers to idents in the 'variant.feature.type' namespace |
| gene :variant/gene | gene | one | The gene for this variant |
| genomic-coordinates :variant/genomic-coordinates | genomic-coordinate | one | The coordinates of this variant |
| id :variant/id | string | oneunique identity | Globally unique id for this variant. This is constructed by joining using '/' the coordinates, ref-allele and alt-allele |
| impact :variant/impact | variant.impact | one | The impact modifier for this variant. Refers to entities in the variant.impact namespace |
| max-af :variant/max-af | float | one | Maximum reference allele frequency, as annotated by VEP or snpEff. This is a measurement of how prevalent the allele is in reference populations (therefore assumed non-lethal germline variant). |
| neo-antigens :variant/neo-antigens | neo-antigen | many | The list of neo-antigens associated with this variant |
| partner-genes :variant/partner-genes | gene | many | Other genes impacted by this variant, as in large deletions, fusions, and other structural re-arrangements. |
| partner-genomic-coordinates :variant/partner-genomic-coordinates | genomic-coordinate | one | Other coordinates impacted by a structural variant, e.g. novel fusion / breakend partners. |
| publication :variant/publication | string | many | DOI of publication associated with this variant, as a string |
| quick-summary :variant/quick-summary | string | one | Summarized name for variant as [hgnc_symbol]-[HGSVp] |
| ref-allele :variant/ref-allele | string | one | The reference allele for this variant |
| ref-amino-acid :variant/ref-amino-acid | string | one | The reference one letter coded amino acid sequence for this variant (ie A, R) |
| so-consequences :variant/so-consequences | so-sequence-feature | many | The functional consequence of the variant, in sequence ontology terms (http://www.sequenceontology.org/). Refers to so-sequence-feature entities |
| structural-category :variant/structural-category | variant.structural-category | one | The category (as enum) for this structural variant, in variant.structural-category namespace. All structural variants must have this attribute. |
| type :variant/type | variant.type | one | The type of this variant, refers to idents in the 'variant.type' namespace |
Referenced by
| Attribute | On kind | Cardinality |
|---|---|---|
:measurement/variant | measurement | one |