Variants¶
The variants endpoint allows users to enumerate all of the variants present in CIViC as well as retrieve more detailed information on a specific variant. A common use case would be to get a list of variants for a gene using the genes endpoint and then fetching detailed information for each variant via the variants endpoint.
Get a list of variants¶
This endpoint returns a listing of variants in CIViC that contain at least one evidence item. This index style endpoint is paginated by default. You can use the count and page parameters or the previous and next links to iterate through all the variants.
HTTP Request Format
GET https://civicdb.org/api/variants
Query Parameters
Parameter |
Default |
Description |
|---|---|---|
page |
1 |
Which page of results to return |
count |
25 |
How many variants to return on a single page |
Example Request
curl https://civicdb.org/api/variants?count=1
Example Response
{
"_meta": {
"current_page": 1,
"per_page": "1",
"total_pages": 3163,
"total_count": 3163,
"links": {
"next": "https://v1.civicdb.org/api/variants?count=1&page=2",
"previous": null
}
},
"records": [
{
"id": 1,
"entrez_name": "ABL1",
"entrez_id": 25,
"name": "BCR::ABL",
"description": "The BCR-ABL fusion protein, commonly referred to as the Philadelphia chromosome, is one of the most studied fusion genes in cancer. It has widely been considered the initiating event in chronic myelogenous leukemia (CML). However, despite its ability to initiate disease in mice, its status as an initiating mutation is in dispute. In what is commonly used as the poster-child for targeted therapeutics, the development and use of imatinib in the clinic has led to profound improvements in the prognosis of the disease. However, imatinib resistance is still seen in patients with mutations in the ABL kinase domain of the fusion, most notably the T315I variant. In patients resistant to imatinib, either acquired or otherwise, second generation BCR-ABL TKI's (dasatinib and nilotinib) have seen some success in delivering a tumor response. Third generation ABL1 inhibitor ponatinib is the only FDA approved drug with activity against T315I . However due to risk of life-threatening blood clots and severe narrowing of blood vessels ponatinib is ONLY approved for T315I-positive CML or T315I-positive Ph+ ALL or in cases of CML, Ph+ ALL with resistance or intolerance to other approved ABL1 inhibitors.",
"gene_id": 4,
"type": "variant",
"variant_types": [
{
"id": 120,
"name": "transcript_fusion",
"display_name": "Transcript Fusion",
"so_id": "SO:0001886",
"description": "A feature fusion where the deletion brings together transcript regions.",
"url": "http://www.sequenceontology.org/browser/current_svn/term/SO:0001886",
"root_concept": {
"so_id": "SO:0001060",
"name": "Sequence Variant"
}
}
],
"civic_actionability_score": 255.5,
"flagged": false,
"updated_at": "2022-03-10T22:27:25.538Z",
"coordinates": {
"chromosome": "22",
"start": 23522397,
"stop": 23632600,
"reference_bases": null,
"variant_bases": null,
"representative_transcript": "ENST00000305877.8",
"chromosome2": "9",
"start2": 133729451,
"stop2": 133763063,
"representative_transcript2": "ENST00000318560.5",
"ensembl_version": 75,
"reference_build": "GRCh37"
}
}
]
}
Get details for a specific variant¶
This endpoint retrieves details about a specific variant, given its internal CIViC id.
HTTP Request Format
GET https://civicdb.org/api/variants/:id
Example Request
curl https://civicdb.org/api/variants/13
Example Response
{
"id": 13,
"entrez_name": "BRAF",
"entrez_id": 673,
"name": "V600E and V600M",
"description": "A case study of a single patient harboring both a V600E and a V600M mutation, dabrafenib was shown to acheive clinical response.",
"gene_id": 5,
"type": "variant",
"variant_types": [
{
"id": 47,
"name": "missense_variant",
"display_name": "Missense Variant",
"so_id": "SO:0001583",
"description": "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved.",
"url": "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583",
"root_concept": {
"so_id": "SO:0001060",
"name": "Sequence Variant"
}
}
],
"civic_actionability_score": 2.5,
"flagged": false,
"updated_at": "2021-04-14T05:00:56.973Z",
"coordinates": {
"chromosome": "7",
"start": 140453135,
"stop": 140453137,
"reference_bases": null,
"variant_bases": null,
"representative_transcript": "ENST00000288602.6",
"chromosome2": null,
"start2": null,
"stop2": null,
"representative_transcript2": null,
"ensembl_version": 75,
"reference_build": "GRCh37"
},
"evidence_items": [
{
"id": 73,
"name": "EID73",
"description": "A single 66-year old male patient with advanced melanoma thought to have concomitant BRAF V600E and V600M mutations responded rapidly to dabrafenib. His shoulder lesion reduced by 60% after 1 week of therapy and was gone after 1 month.",
"disease": {
"id": 7,
"name": "Melanoma",
"display_name": "Melanoma",
"doid": "1909",
"url": "http://disease-ontology.org/?id=DOID:1909"
},
"drugs": [
{
"id": 22,
"name": "Dabrafenib",
"ncit_id": "C82386",
"aliases": [
"GSK2118436",
"GSK-2118436A",
"GSK-2118436",
"BRAF Inhibitor GSK2118436",
"Benzenesulfonamide, N-(3-(5-(2-amino-4-pyrimidinyl)-2-(1,1-dimethylethyl)-4-thiazolyl)-2-fluorophenyl)-2,6-difluoro-"
]
}
],
"rating": 1,
"evidence_level": "C",
"evidence_type": "Predictive",
"clinical_significance": "Sensitivity/Response",
"evidence_direction": "Supports",
"variant_origin": "Somatic",
"drug_interaction_type": null,
"status": "accepted",
"open_change_count": 0,
"type": "evidence",
"source": {
"id": 88,
"name": "Overwhelming response to Dabrafenib in a patient with double BRAF mutation (V600E; V600M) metastatic malignant melanoma.",
"citation": "Ponti et al., 2012, J Hematol Oncol",
"citation_id": "23031422",
"source_type": "PubMed",
"asco_abstract_id": null,
"source_url": "http://www.ncbi.nlm.nih.gov/pubmed/23031422",
"open_access": true,
"pmc_id": "PMC3473234",
"publication_date": {
"year": 2012
},
"journal": "J Hematol Oncol",
"full_journal_title": "Journal of hematology & oncology",
"status": "fully curated",
"is_review": false,
"clinical_trials": []
},
"flagged": false,
"variant_id": 13,
"phenotypes": [],
"updated_at": "2021-04-14T17:31:44.639Z"
}
],
"variant_groups": [
{
"id": 5,
"name": "Other V600's",
"description": "While BRAF V600E is nearly ubiquitous in many cancer types, other V600 variants have also been observed and studied to a lesser degree. At first approximation, many of these variants seem to behave similarly to V600E, and treatment with dabrafenib has been shown to be effective. ",
"variants": [
{
"id": 11,
"entrez_name": "BRAF",
"entrez_id": 673,
"name": "V600D",
"description": "Patients harboring mutations in valine 600 residue of BRAF have been shown to be sensitive to dabrafenib. For more information on the V600 locus, see the V600E entry.",
"gene_id": 5,
"type": "variant",
"variant_types": [
{
"id": 47,
"name": "missense_variant",
"display_name": "Missense Variant",
"so_id": "SO:0001583",
"description": "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved.",
"url": "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583",
"root_concept": {
"so_id": "SO:0001060",
"name": "Sequence Variant"
}
}
],
"civic_actionability_score": 47.0,
"flagged": false,
"updated_at": "2020-11-21T22:43:17.643Z",
"coordinates": {
"chromosome": "7",
"start": 140453135,
"stop": 140453136,
"reference_bases": "CA",
"variant_bases": "AT",
"representative_transcript": "ENST00000288602.6",
"chromosome2": null,
"start2": null,
"stop2": null,
"representative_transcript2": null,
"ensembl_version": 75,
"reference_build": "GRCh37"
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},
{
"id": 13,
"entrez_name": "BRAF",
"entrez_id": 673,
"name": "V600E and V600M",
"description": "A case study of a single patient harboring both a V600E and a V600M mutation, dabrafenib was shown to acheive clinical response.",
"gene_id": 5,
"type": "variant",
"variant_types": [
{
"id": 47,
"name": "missense_variant",
"display_name": "Missense Variant",
"so_id": "SO:0001583",
"description": "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved.",
"url": "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583",
"root_concept": {
"so_id": "SO:0001060",
"name": "Sequence Variant"
}
}
],
"civic_actionability_score": 2.5,
"flagged": false,
"updated_at": "2021-04-14T05:00:56.973Z",
"coordinates": {
"chromosome": "7",
"start": 140453135,
"stop": 140453137,
"reference_bases": null,
"variant_bases": null,
"representative_transcript": "ENST00000288602.6",
"chromosome2": null,
"start2": null,
"stop2": null,
"representative_transcript2": null,
"ensembl_version": 75,
"reference_build": "GRCh37"
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},
{
"id": 17,
"entrez_name": "BRAF",
"entrez_id": 673,
"name": "V600",
"description": "BRAF mutations of the valine 600 residue have been shown to be recurrent in many cancer types. Of the V600 mutations, V600E is the most widely researched. V600 mutations as a whole have been correlated to poorer prognosis in colorectal and papilarry thyroid cancers. V600 mutations have also been shown to confer sensitivity to the BRAF inhibitor dabrafenib. For a more detailed summary, click the individual mutations.",
"gene_id": 5,
"type": "variant",
"variant_types": [
{
"id": 103,
"name": "protein_altering_variant",
"display_name": "Protein Altering Variant",
"so_id": "SO:0001818",
"description": "A sequence_variant which is predicted to change the protein encoded in the coding sequence.",
"url": "http://www.sequenceontology.org/browser/current_svn/term/SO:0001818",
"root_concept": {
"so_id": "SO:0001060",
"name": "Sequence Variant"
}
}
],
"civic_actionability_score": 460.0,
"flagged": false,
"updated_at": "2020-12-10T20:13:06.813Z",
"coordinates": {
"chromosome": "7",
"start": 140453136,
"stop": 140453137,
"reference_bases": null,
"variant_bases": null,
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"chromosome2": null,
"start2": null,
"stop2": null,
"representative_transcript2": null,
"ensembl_version": 75,
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},
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"id": 288,
"entrez_name": "BRAF",
"entrez_id": 673,
"name": "L597R",
"description": "",
"gene_id": 5,
"type": "variant",
"variant_types": [
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"id": 47,
"name": "missense_variant",
"display_name": "Missense Variant",
"so_id": "SO:0001583",
"description": "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved.",
"url": "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583",
"root_concept": {
"so_id": "SO:0001060",
"name": "Sequence Variant"
}
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],
"civic_actionability_score": 12.0,
"flagged": false,
"updated_at": "2018-11-30T14:45:06.389Z",
"coordinates": {
"chromosome": "7",
"start": 140453145,
"stop": 140453145,
"reference_bases": "A",
"variant_bases": "C",
"representative_transcript": "ENST00000288602.6",
"chromosome2": null,
"start2": null,
"stop2": null,
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"ensembl_version": 75,
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},
{
"id": 563,
"entrez_name": "BRAF",
"entrez_id": 673,
"name": "V600K",
"description": "",
"gene_id": 5,
"type": "variant",
"variant_types": [
{
"id": 47,
"name": "missense_variant",
"display_name": "Missense Variant",
"so_id": "SO:0001583",
"description": "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved.",
"url": "http://www.sequenceontology.org/browser/current_svn/term/SO:0001583",
"root_concept": {
"so_id": "SO:0001060",
"name": "Sequence Variant"
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"civic_actionability_score": 107.5,
"flagged": false,
"updated_at": "2021-01-05T22:01:14.757Z",
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],
"type": "variant_group",
"flagged": false,
"updated_at": "2015-06-21T16:49:55.193Z"
}
],
"assertions": [],
"variant_aliases": [],
"hgvs_expressions": [],
"clinvar_entries": [
"44815",
"13961"
],
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