Variant List
This API endpoint handles listing (/variants) and retrieval (/variants/<ID>/) of genetic variants from the database
GET /api/genes/VAPB/variants/?format=api
{ "data": [ { "type": "SmallVariant", "id": "533", "attributes": { "frequencies": { "KGP_genomes_maf": 0.001, "KGP_genomes_AFR_maf": 0.0008, "KGP_genomes_AMR_maf": 0.0, "KGP_genomes_EAS_maf": 0.0, "KGP_genomes_EUR_maf": 0.004, "KGP_genomes_SAS_maf": 0.0, "gnomad_maf": 0.001266, "gnomad_AFR_maf": 0.0004929, "gnomad_AMR_maf": 0.0001446, "gnomad_ASJ_maf": 0.0, "gnomad_EAS_maf": 0.0, "gnomad_FIN_maf": 0.0005082, "gnomad_NFE_maf": 0.002535, "gnomad_OTH_maf": 0.0009785, "gnomad_SAS_maf": 0.0, "ESP_AA_maf": 0.000227, "ESP_EA_maf": 0.001628 }, "predictions": { "sift_prediction": "Deleterious", "pp2_hvar_prediction": "Benign", "cadd_prediction": 3.401208, "mutationtaster_prediction": "Disease causing" }, "status": "CU", "genomic_position_hg19": 57016076, "genomic_position_hg38": 58441020, "chromosome": "20", "annotation_flag": "automatically_attributed", "lastmodified": "2023-06-06T16:57:43.659363", "ref_allele": "G", "alt_allele": "A", "cdna_change": "c.510G>A", "protein_change": "p.Met170Ile", "transcript_id": "NM_004738.4", "dbsnp_id": "rs143144050", "variant_effect": "missense" }, "relationships": { "in_combination": { "meta": { "count": 2 }, "data": [ { "type": "Combination", "id": "OLI274" }, { "type": "Combination", "id": "OLI279" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/533/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/533/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/533/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/533/gene/?format=api" }, "data": { "type": "Gene", "id": "VAPB" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/533/?format=api" } }, { "type": "SmallVariant", "id": "1819", "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": 5.567e-05, "gnomad_AFR_maf": 0.0, "gnomad_AMR_maf": 0.0, "gnomad_ASJ_maf": 9.921e-05, "gnomad_EAS_maf": 0.0, "gnomad_FIN_maf": 0.0001386, "gnomad_NFE_maf": 8.79e-05, "gnomad_OTH_maf": 0.0, "gnomad_SAS_maf": 0.0, "ESP_AA_maf": 0.0, "ESP_EA_maf": 0.0001163 }, "predictions": { "sift_prediction": "Tolerated", "pp2_hvar_prediction": "Benign", "cadd_prediction": 0.961187, "mutationtaster_prediction": null }, "status": "CU", "genomic_position_hg19": 57019259, "genomic_position_hg38": 58444203, "chromosome": "20", "annotation_flag": "automatically_attributed", "lastmodified": "2023-06-06T16:57:51.489243", "ref_allele": "G", "alt_allele": "A", "cdna_change": null, "protein_change": "p.Val234Ile", "transcript_id": null, "dbsnp_id": "rs149215094", "variant_effect": "missense" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI830" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/1819/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/1819/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/1819/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/1819/gene/?format=api" }, "data": { "type": "Gene", "id": "VAPB" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/1819/?format=api" } }, { "type": "SmallVariant", "id": "2092", "attributes": { "frequencies": { "KGP_genomes_maf": 0.0048, "KGP_genomes_AFR_maf": 0.0008, "KGP_genomes_AMR_maf": 0.0086, "KGP_genomes_EAS_maf": 0.0, "KGP_genomes_EUR_maf": 0.0119, "KGP_genomes_SAS_maf": 0.0051, "gnomad_maf": 0.008981, "gnomad_AFR_maf": 0.002326, "gnomad_AMR_maf": 0.006741, "gnomad_ASJ_maf": 0.02732, "gnomad_EAS_maf": 9.498e-05, "gnomad_FIN_maf": 0.00167, "gnomad_NFE_maf": 0.01092, "gnomad_OTH_maf": 0.01012, "gnomad_SAS_maf": 0.007514, "ESP_AA_maf": null, "ESP_EA_maf": null }, "predictions": { "sift_prediction": null, "pp2_hvar_prediction": null, "cadd_prediction": 1.419745, "mutationtaster_prediction": "Polymorphism" }, "status": "CU", "genomic_position_hg19": 57020044, "genomic_position_hg38": 58444988, "chromosome": "20", "annotation_flag": null, "lastmodified": "2023-06-06T16:57:53.163179", "ref_allele": "C", "alt_allele": "G", "cdna_change": "c.*753C>G", "protein_change": null, "transcript_id": null, "dbsnp_id": "NA", "variant_effect": null }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI967" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/2092/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/2092/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/2092/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/2092/gene/?format=api" }, "data": { "type": "Gene", "id": "VAPB" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/2092/?format=api" } }, { "type": "SmallVariant", "id": "2094", "attributes": { "frequencies": { "KGP_genomes_maf": 0.0082, "KGP_genomes_AFR_maf": 0.0, "KGP_genomes_AMR_maf": 0.0043, "KGP_genomes_EAS_maf": 0.0, "KGP_genomes_EUR_maf": 0.0119, "KGP_genomes_SAS_maf": 0.0266, "gnomad_maf": 0.01501, "gnomad_AFR_maf": 0.001972, "gnomad_AMR_maf": 0.006694, "gnomad_ASJ_maf": 0.01384, "gnomad_EAS_maf": 0.0, "gnomad_FIN_maf": 0.00984, "gnomad_NFE_maf": 0.01689, "gnomad_OTH_maf": 0.01153, "gnomad_SAS_maf": 0.03293, "ESP_AA_maf": null, "ESP_EA_maf": null }, "predictions": { "sift_prediction": null, "pp2_hvar_prediction": null, "cadd_prediction": -0.249712, "mutationtaster_prediction": "Polymorphism" }, "status": "CU", "genomic_position_hg19": 57025473, "genomic_position_hg38": 58450417, "chromosome": "20", "annotation_flag": null, "lastmodified": "2023-06-06T16:57:53.175672", "ref_allele": "C", "alt_allele": "T", "cdna_change": "c.*6182C>T", "protein_change": null, "transcript_id": null, "dbsnp_id": "NA", "variant_effect": null }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI968" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/2094/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/2094/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/2094/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/2094/gene/?format=api" }, "data": { "type": "Gene", "id": "VAPB" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/2094/?format=api" } }, { "type": "SmallVariant", "id": "2102", "attributes": { "frequencies": { "KGP_genomes_maf": 0.1284, "KGP_genomes_AFR_maf": 0.1044, "KGP_genomes_AMR_maf": 0.1671, "KGP_genomes_EAS_maf": 0.2718, "KGP_genomes_EUR_maf": 0.0895, "KGP_genomes_SAS_maf": 0.0256, "gnomad_maf": 0.1045, "gnomad_AFR_maf": 0.09457, "gnomad_AMR_maf": 0.1615, "gnomad_ASJ_maf": 0.07463, "gnomad_EAS_maf": 0.2564, "gnomad_FIN_maf": 0.07241, "gnomad_NFE_maf": 0.08792, "gnomad_OTH_maf": 0.108, "gnomad_SAS_maf": 0.03308, "ESP_AA_maf": null, "ESP_EA_maf": null }, "predictions": { "sift_prediction": null, "pp2_hvar_prediction": null, "cadd_prediction": 1.23592, "mutationtaster_prediction": "Polymorphism" }, "status": "CU", "genomic_position_hg19": 57020556, "genomic_position_hg38": 58445500, "chromosome": "20", "annotation_flag": null, "lastmodified": "2023-06-06T16:57:53.225971", "ref_allele": "G", "alt_allele": "C", "cdna_change": "c.*1265G>C", "protein_change": null, "transcript_id": null, "dbsnp_id": "NA", "variant_effect": null }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI970" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/2102/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/2102/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/2102/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/2102/gene/?format=api" }, "data": { "type": "Gene", "id": "VAPB" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/2102/?format=api" } }, { "type": "SmallVariant", "id": "2103", "attributes": { "frequencies": { "KGP_genomes_maf": 0.1108, "KGP_genomes_AFR_maf": 0.0378, "KGP_genomes_AMR_maf": 0.1657, "KGP_genomes_EAS_maf": 0.2718, "KGP_genomes_EUR_maf": 0.0905, "KGP_genomes_SAS_maf": 0.0256, "gnomad_maf": 0.102, "gnomad_AFR_maf": 0.03578, "gnomad_AMR_maf": 0.1592, "gnomad_ASJ_maf": 0.07379, "gnomad_EAS_maf": 0.2585, "gnomad_FIN_maf": 0.07222, "gnomad_NFE_maf": 0.08699, "gnomad_OTH_maf": 0.1061, "gnomad_SAS_maf": 0.03288, "ESP_AA_maf": null, "ESP_EA_maf": null }, "predictions": { "sift_prediction": null, "pp2_hvar_prediction": null, "cadd_prediction": -0.209779, "mutationtaster_prediction": "Polymorphism" }, "status": "CU", "genomic_position_hg19": 57022110, "genomic_position_hg38": 58447054, "chromosome": "20", "annotation_flag": null, "lastmodified": "2023-06-06T16:57:53.232265", "ref_allele": "A", "alt_allele": "G", "cdna_change": "c.*2819A>G", "protein_change": null, "transcript_id": null, "dbsnp_id": "NA", "variant_effect": null }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI970" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/2103/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/2103/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/2103/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/2103/gene/?format=api" }, "data": { "type": "Gene", "id": "VAPB" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/2103/?format=api" } }, { "type": "SmallVariant", "id": "2104", "attributes": { "frequencies": { "KGP_genomes_maf": 0.1396, "KGP_genomes_AFR_maf": 0.1241, "KGP_genomes_AMR_maf": 0.1816, "KGP_genomes_EAS_maf": 0.2728, "KGP_genomes_EUR_maf": 0.1054, "KGP_genomes_SAS_maf": 0.0286, "gnomad_maf": 0.1116, "gnomad_AFR_maf": 0.1066, "gnomad_AMR_maf": 0.1683, "gnomad_ASJ_maf": 0.0745, "gnomad_EAS_maf": 0.2589, "gnomad_FIN_maf": 0.07931, "gnomad_NFE_maf": 0.09727, "gnomad_OTH_maf": 0.1148, "gnomad_SAS_maf": 0.03373, "ESP_AA_maf": null, "ESP_EA_maf": null }, "predictions": { "sift_prediction": null, "pp2_hvar_prediction": null, "cadd_prediction": -0.178397, "mutationtaster_prediction": "Polymorphism" }, "status": "CU", "genomic_position_hg19": 57023811, "genomic_position_hg38": 58448755, "chromosome": "20", "annotation_flag": null, "lastmodified": "2023-06-06T16:57:53.238588", "ref_allele": "T", "alt_allele": "C", "cdna_change": "c.*4520T>C", "protein_change": null, "transcript_id": null, "dbsnp_id": "NA", "variant_effect": null }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI970" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/2104/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/2104/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/2104/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/2104/gene/?format=api" }, "data": { "type": "Gene", "id": "VAPB" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/2104/?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 } }