Variant List
This API endpoint handles listing (/variants) and retrieval (/variants/<ID>/) of genetic variants from the database
GET /api/genes/BBS5/variants/?format=api
{ "data": [ { "type": "CopyNumberVariant", "id": "1364", "attributes": { "status": "CU", "genomic_position_hg19": 170355189, "genomic_position_hg38": 169498679, "chromosome": "2", "annotation_flag": "cnv", "lastmodified": "2021-10-18T11:01:08.290258", "location": "exon8_12", "sequence": "exon8_12", "number_of_repeats": null, "type_cnv": "deletion" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI621" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/1364/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/1364/combinations/?format=api" } }, "gene_name": { "data": { "type": "Gene", "id": "BBS5" }, "links": { "related": "https://olida.ibsquare.be/api/genes/BBS5/?format=api" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/1364/?format=api" } }, { "type": "SmallVariant", "id": "169", "attributes": { "frequencies": { "KGP_genomes_maf": 0.0022, "KGP_genomes_AFR_maf": 0.0, "KGP_genomes_AMR_maf": 0.0043, "KGP_genomes_EAS_maf": 0.0, "KGP_genomes_EUR_maf": 0.007, "KGP_genomes_SAS_maf": 0.001, "gnomad_maf": 0.00419, "gnomad_AFR_maf": 0.0004311, "gnomad_AMR_maf": 0.001649, "gnomad_ASJ_maf": 0.004564, "gnomad_EAS_maf": 5.437e-05, "gnomad_FIN_maf": 0.004805, "gnomad_NFE_maf": 0.006979, "gnomad_OTH_maf": 0.003264, "gnomad_SAS_maf": 0.0008169, "ESP_AA_maf": 0.000227, "ESP_EA_maf": 0.00698 }, "predictions": { "sift_prediction": "Deleterious", "pp2_hvar_prediction": "Damaging", "cadd_prediction": 3.620418, "mutationtaster_prediction": "Polymorphism" }, "status": "CU", "genomic_position_hg19": 170350279, "genomic_position_hg38": 169493769, "chromosome": "2", "annotation_flag": "automatically_attributed", "lastmodified": "2023-06-06T16:57:41.512539", "ref_allele": "A", "alt_allele": "G", "cdna_change": null, "protein_change": "p.Asn184Ser", "transcript_id": null, "dbsnp_id": "rs137853921", "variant_effect": "missense" }, "relationships": { "in_combination": { "meta": { "count": 2 }, "data": [ { "type": "Combination", "id": "OLI083" }, { "type": "Combination", "id": "OLI618" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/169/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/169/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/169/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/169/gene/?format=api" }, "data": { "type": "Gene", "id": "BBS5" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/169/?format=api" } }, { "type": "SmallVariant", "id": "1356", "attributes": { "frequencies": { "KGP_genomes_maf": 0.0024, "KGP_genomes_AFR_maf": 0.0, "KGP_genomes_AMR_maf": 0.0173, "KGP_genomes_EAS_maf": 0.0, "KGP_genomes_EUR_maf": 0.0, "KGP_genomes_SAS_maf": 0.0, "gnomad_maf": 0.006341, "gnomad_AFR_maf": 0.0007392, "gnomad_AMR_maf": 0.04477, "gnomad_ASJ_maf": 0.0, "gnomad_EAS_maf": 0.0, "gnomad_FIN_maf": 0.0, "gnomad_NFE_maf": 6.162e-05, "gnomad_OTH_maf": 0.004405, "gnomad_SAS_maf": 0.0, "ESP_AA_maf": 0.000227, "ESP_EA_maf": 0.000349 }, "predictions": { "sift_prediction": "Tolerated", "pp2_hvar_prediction": "Possibly Damaging", "cadd_prediction": 3.386821, "mutationtaster_prediction": "Polymorphism" }, "status": "CU", "genomic_position_hg19": 170350312, "genomic_position_hg38": 169493802, "chromosome": "2", "annotation_flag": "automatically_attributed", "lastmodified": "2023-06-06T16:57:48.646670", "ref_allele": "A", "alt_allele": "G", "cdna_change": "c.584A>G", "protein_change": "p.Asp195Gly", "transcript_id": "NM_152384.2", "dbsnp_id": "rs143191074", "variant_effect": "missense" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI617" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/1356/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/1356/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/1356/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/1356/gene/?format=api" }, "data": { "type": "Gene", "id": "BBS5" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/1356/?format=api" } }, { "type": "SmallVariant", "id": "2426", "attributes": { "frequencies": { "KGP_genomes_maf": 0.0022, "KGP_genomes_AFR_maf": 0.0, "KGP_genomes_AMR_maf": 0.0043, "KGP_genomes_EAS_maf": 0.0, "KGP_genomes_EUR_maf": 0.007, "KGP_genomes_SAS_maf": 0.001, "gnomad_maf": 0.00419, "gnomad_AFR_maf": 0.0004311, "gnomad_AMR_maf": 0.001649, "gnomad_ASJ_maf": 0.004564, "gnomad_EAS_maf": 5.437e-05, "gnomad_FIN_maf": 0.004805, "gnomad_NFE_maf": 0.006979, "gnomad_OTH_maf": 0.003264, "gnomad_SAS_maf": 0.0008169, "ESP_AA_maf": 0.000227, "ESP_EA_maf": 0.00698 }, "predictions": { "sift_prediction": "Deleterious", "pp2_hvar_prediction": "Damaging", "cadd_prediction": 3.620418, "mutationtaster_prediction": "Polymorphism" }, "status": "CU", "genomic_position_hg19": 170350279, "genomic_position_hg38": 169493769, "chromosome": "2", "annotation_flag": null, "lastmodified": "2023-06-06T16:57:55.188012", "ref_allele": "A", "alt_allele": "G", "cdna_change": "c.551A>G", "protein_change": "p.Asn184Ser", "transcript_id": "NM_152384.3", "dbsnp_id": "rs137853921", "variant_effect": null }, "relationships": { "in_combination": { "meta": { "count": 2 }, "data": [ { "type": "Combination", "id": "OLI1125" }, { "type": "Combination", "id": "OLI1448" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/2426/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/2426/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/2426/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/2426/gene/?format=api" }, "data": { "type": "Gene", "id": "BBS5" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/2426/?format=api" } }, { "type": "SmallVariant", "id": "2441", "attributes": { "frequencies": { "KGP_genomes_maf": 0.0004, "KGP_genomes_AFR_maf": 0.0, "KGP_genomes_AMR_maf": 0.0, "KGP_genomes_EAS_maf": 0.0, "KGP_genomes_EUR_maf": 0.001, "KGP_genomes_SAS_maf": 0.001, "gnomad_maf": 0.001066, "gnomad_AFR_maf": 0.0003077, "gnomad_AMR_maf": 0.001215, "gnomad_ASJ_maf": 0.0, "gnomad_EAS_maf": 0.0, "gnomad_FIN_maf": 0.0001386, "gnomad_NFE_maf": 0.001513, "gnomad_OTH_maf": 0.001468, "gnomad_SAS_maf": 0.001209, "ESP_AA_maf": 0.0006809, "ESP_EA_maf": 0.001047 }, "predictions": { "sift_prediction": "Tolerated", "pp2_hvar_prediction": "Benign", "cadd_prediction": 2.73111, "mutationtaster_prediction": "Polymorphism" }, "status": "CU", "genomic_position_hg19": 170356065, "genomic_position_hg38": 169499555, "chromosome": "2", "annotation_flag": null, "lastmodified": "2023-06-06T16:57:55.272938", "ref_allele": "A", "alt_allele": "G", "cdna_change": "c.751A>G", "protein_change": "p.Asn251Asp", "transcript_id": null, "dbsnp_id": "NA", "variant_effect": null }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI1134" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/2441/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/2441/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/2441/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/2441/gene/?format=api" }, "data": { "type": "Gene", "id": "BBS5" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/2441/?format=api" } }, { "type": "SmallVariant", "id": "3027", "attributes": { "frequencies": { "KGP_genomes_maf": 0.005, "KGP_genomes_AFR_maf": 0.0008, "KGP_genomes_AMR_maf": 0.0086, "KGP_genomes_EAS_maf": 0.0, "KGP_genomes_EUR_maf": 0.0099, "KGP_genomes_SAS_maf": 0.0082, "gnomad_maf": 0.006557, "gnomad_AFR_maf": 0.002421, "gnomad_AMR_maf": 0.002931, "gnomad_ASJ_maf": 0.003479, "gnomad_EAS_maf": 0.001143, "gnomad_FIN_maf": 0.01049, "gnomad_NFE_maf": 0.008841, "gnomad_OTH_maf": 0.005077, "gnomad_SAS_maf": 0.006121, "ESP_AA_maf": null, "ESP_EA_maf": null }, "predictions": { "sift_prediction": "Tolerated", "pp2_hvar_prediction": "Benign", "cadd_prediction": 4.520405, "mutationtaster_prediction": "Polymorphism" }, "status": "CU", "genomic_position_hg19": 170354138, "genomic_position_hg38": 169497628, "chromosome": "2", "annotation_flag": null, "lastmodified": "2023-06-06T16:57:58.678414", "ref_allele": "G", "alt_allele": "A", "cdna_change": "c.620G>A", "protein_change": "p.Arg207His", "transcript_id": "NM_152384.3", "dbsnp_id": "NA", "variant_effect": null }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI1438" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/3027/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/3027/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/3027/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/3027/gene/?format=api" }, "data": { "type": "Gene", "id": "BBS5" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/3027/?format=api" } }, { "type": "SmallVariant", "id": "3497", "attributes": { "frequencies": { "KGP_genomes_maf": null, "KGP_genomes_AFR_maf": null, "KGP_genomes_AMR_maf": null, "KGP_genomes_EAS_maf": null, "KGP_genomes_EUR_maf": null, "KGP_genomes_SAS_maf": null, "gnomad_maf": null, "gnomad_AFR_maf": null, "gnomad_AMR_maf": null, "gnomad_ASJ_maf": null, "gnomad_EAS_maf": null, "gnomad_FIN_maf": null, "gnomad_NFE_maf": null, "gnomad_OTH_maf": null, "gnomad_SAS_maf": null, "ESP_AA_maf": null, "ESP_EA_maf": null }, "predictions": { "sift_prediction": null, "pp2_hvar_prediction": null, "cadd_prediction": 5.039965, "mutationtaster_prediction": "Disease causing" }, "status": "CU", "genomic_position_hg19": 170343633, "genomic_position_hg38": 169487123, "chromosome": "2", "annotation_flag": null, "lastmodified": "2024-02-29T15:02:27.339514", "ref_allele": "GA", "alt_allele": "G", "cdna_change": "c.198del", "protein_change": "p.Val67SerfsTer11", "transcript_id": "NM_152384.2", "dbsnp_id": "NA", "variant_effect": null }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI1664" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/3497/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/3497/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/3497/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/3497/gene/?format=api" }, "data": { "type": "Gene", "id": "BBS5" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/3497/?format=api" } } ], "meta": { "database_name": "OLIgogenic diseases DAtabase (OLIDA)", "resource_url": "olida.ibsquare.be", "api_release_year": "2021", "api_developer": [ [ "Arnau Dillen", "arnau.dillen@ulb.ac.be" ], [ "Charlotte Nachtegael", "charlotte.nachtegael@ulb.be" ] ], "api_version": "0.3", "api_maintainers": [ [ "Charlotte Nachtegael", "charlotte.nachtegael@ulb.be" ] ], "api_documentation": [ "olida.ibsquare.be/api/swagger", "olida.ibsquare.be/api/redoc" ], "copyright": "Copyright (c) 2025 · OLIDA All Rights Reserved.", "license": "CC Attribution-NonCommercial 4.0 International License", "ontologies": { "ORDO": "http://bioportal.bioontology.org/ontologies/ORDO", "GENO": "http://purl.obolibrary.org/obo/geno.owl", "MI": "http://purl.obolibrary.org/obo/mi.owl", "NCIT": "http://purl.obolibrary.org/obo/ncit.owl", "OGI": "http://purl.obolibrary.org/obo/ogi.owl", "OGG": "http://purl.obolibrary.org/obo/ogg.owl" }, "relevant_publications_doi": [ "10.1093/nar/gkv1068", "10.1093/database/baac023" ], "Variant serializers": [ "SmallVariantSerializer", "CopyNumberVariantSerializer" ], "size": 7 } }