Variant List
This API endpoint handles listing (/variants) and retrieval (/variants/<ID>/) of genetic variants from the database
GET /api/genes/NPHS2/variants/?format=api
{ "data": [ { "type": "SmallVariant", "id": "496", "attributes": { "frequencies": { "KGP_genomes_maf": 0.0146, "KGP_genomes_AFR_maf": 0.003, "KGP_genomes_AMR_maf": 0.013, "KGP_genomes_EAS_maf": 0.0, "KGP_genomes_EUR_maf": 0.0417, "KGP_genomes_SAS_maf": 0.0184, "gnomad_maf": 0.03045, "gnomad_AFR_maf": 0.006215, "gnomad_AMR_maf": 0.01284, "gnomad_ASJ_maf": 0.05236, "gnomad_EAS_maf": 0.0001088, "gnomad_FIN_maf": 0.06972, "gnomad_NFE_maf": 0.03576, "gnomad_OTH_maf": 0.02947, "gnomad_SAS_maf": 0.02697, "ESP_AA_maf": 0.007717, "ESP_EA_maf": 0.03756 }, "predictions": { "sift_prediction": "Tolerated", "pp2_hvar_prediction": "Benign", "cadd_prediction": 3.02406, "mutationtaster_prediction": "Disease causing" }, "status": "CU", "genomic_position_hg19": 179526214, "genomic_position_hg38": 179557079, "chromosome": "1", "annotation_flag": "automatically_attributed", "lastmodified": "2023-06-06T16:57:43.450968", "ref_allele": "C", "alt_allele": "T", "cdna_change": "c.623G>A", "protein_change": "p.Arg229Gln", "transcript_id": "None", "dbsnp_id": "rs61747728", "variant_effect": "missense" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI255" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/496/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/496/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/496/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/496/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHS2" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/496/?format=api" } }, { "type": "SmallVariant", "id": "498", "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": 3.979e-06, "gnomad_AFR_maf": 0.0, "gnomad_AMR_maf": 0.0, "gnomad_ASJ_maf": 0.0, "gnomad_EAS_maf": 0.0, "gnomad_FIN_maf": 0.0, "gnomad_NFE_maf": 0.0, "gnomad_OTH_maf": 0.0, "gnomad_SAS_maf": 3.266e-05, "ESP_AA_maf": null, "ESP_EA_maf": null }, "predictions": { "sift_prediction": null, "pp2_hvar_prediction": null, "cadd_prediction": 5.007439, "mutationtaster_prediction": "Disease causing" }, "status": "CU", "genomic_position_hg19": 179530438, "genomic_position_hg38": 179561303, "chromosome": "1", "annotation_flag": "manually_attributed", "lastmodified": "2023-06-06T16:57:43.463819", "ref_allele": "CT", "alt_allele": "C", "cdna_change": "c.436delA", "protein_change": "p.Arg146GlufsTer35", "transcript_id": "NM_014625.4", "dbsnp_id": "rs778201387", "variant_effect": "frameshift" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI256" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/498/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/498/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/498/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/498/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHS2" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/498/?format=api" } }, { "type": "SmallVariant", "id": "500", "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": 0.0005969, "gnomad_AFR_maf": 0.0001233, "gnomad_AMR_maf": 2.893e-05, "gnomad_ASJ_maf": 0.0, "gnomad_EAS_maf": 0.0, "gnomad_FIN_maf": 9.239e-05, "gnomad_NFE_maf": 0.001206, "gnomad_OTH_maf": 0.0009788, "gnomad_SAS_maf": 6.533e-05, "ESP_AA_maf": 0.0, "ESP_EA_maf": 0.0009302 }, "predictions": { "sift_prediction": "Deleterious", "pp2_hvar_prediction": "Damaging", "cadd_prediction": 4.66581, "mutationtaster_prediction": "Disease causing" }, "status": "CU", "genomic_position_hg19": 179530462, "genomic_position_hg38": 179561327, "chromosome": "1", "annotation_flag": "automatically_attributed", "lastmodified": "2023-06-06T16:57:43.476594", "ref_allele": "C", "alt_allele": "T", "cdna_change": "c.413G>A", "protein_change": "p.Arg138Gln", "transcript_id": "NM_014625.3", "dbsnp_id": "rs74315342", "variant_effect": "missense" }, "relationships": { "in_combination": { "meta": { "count": 3 }, "data": [ { "type": "Combination", "id": "OLI257" }, { "type": "Combination", "id": "OLI321" }, { "type": "Combination", "id": "OLI501" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/500/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/500/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/500/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/500/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHS2" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/500/?format=api" } }, { "type": "SmallVariant", "id": "620", "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": 5.174e-05, "gnomad_AFR_maf": 0.0, "gnomad_AMR_maf": 2.894e-05, "gnomad_ASJ_maf": 0.0, "gnomad_EAS_maf": 0.0, "gnomad_FIN_maf": 0.0, "gnomad_NFE_maf": 8.802e-05, "gnomad_OTH_maf": 0.0003268, "gnomad_SAS_maf": 0.0, "ESP_AA_maf": null, "ESP_EA_maf": null }, "predictions": { "sift_prediction": "Tolerated", "pp2_hvar_prediction": "Benign", "cadd_prediction": 1.960955, "mutationtaster_prediction": null }, "status": "CU", "genomic_position_hg19": 179526278, "genomic_position_hg38": 179557143, "chromosome": "1", "annotation_flag": "automatically_attributed", "lastmodified": "2023-06-06T16:57:44.132045", "ref_allele": "C", "alt_allele": "T", "cdna_change": "c.622G>A", "protein_change": "p.Ala208Thr", "transcript_id": "NM_014625.3", "dbsnp_id": "rs200587413", "variant_effect": "missense" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI320" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/620/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/620/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/620/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/620/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHS2" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/620/?format=api" } }, { "type": "SmallVariant", "id": "623", "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": 1.195e-05, "gnomad_AFR_maf": 0.0, "gnomad_AMR_maf": 0.0, "gnomad_ASJ_maf": 0.0, "gnomad_EAS_maf": 0.0, "gnomad_FIN_maf": 0.0, "gnomad_NFE_maf": 2.646e-05, "gnomad_OTH_maf": 0.0, "gnomad_SAS_maf": 0.0, "ESP_AA_maf": null, "ESP_EA_maf": null }, "predictions": { "sift_prediction": null, "pp2_hvar_prediction": null, "cadd_prediction": 2.38273, "mutationtaster_prediction": "Disease causing" }, "status": "CU", "genomic_position_hg19": 179520511, "genomic_position_hg38": 179551376, "chromosome": "1", "annotation_flag": "manually_attributed", "lastmodified": "2023-06-06T16:57:44.152803", "ref_allele": "CA", "alt_allele": "C", "cdna_change": "c.948delT", "protein_change": "p.Ala317LeufsTer31", "transcript_id": "NM_014625.4", "dbsnp_id": "rs775170915", "variant_effect": "frameshift" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI321" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/623/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/623/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/623/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/623/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHS2" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/623/?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": 5 } }