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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 19-48297015-A-AGTGCTGGAGGCAGGGCCG (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=48297015&ref=A&alt=AGTGCTGGAGGCAGGGCCG&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 48297015,
"ref": "A",
"alt": "AGTGCTGGAGGCAGGGCCG",
"effect": "disruptive_inframe_insertion",
"transcript": "NM_001364171.2",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "TGPASST",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ODAD1",
"gene_hgnc_id": 26560,
"hgvs_c": "c.2067_2084dupCGGCCCTGCCTCCAGCAC",
"hgvs_p": "p.Thr695_Gly696insGlyProAlaSerSerThr",
"transcript": "NM_001364171.2",
"protein_id": "NP_001351100.1",
"transcript_support_level": null,
"aa_start": 695,
"aa_end": null,
"aa_length": 707,
"cds_start": 2084,
"cds_end": null,
"cds_length": 2124,
"cdna_start": 2441,
"cdna_end": null,
"cdna_length": 2995,
"mane_select": "ENST00000674294.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "TGPASST",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ODAD1",
"gene_hgnc_id": 26560,
"hgvs_c": "c.2067_2084dupCGGCCCTGCCTCCAGCAC",
"hgvs_p": "p.Thr695_Gly696insGlyProAlaSerSerThr",
"transcript": "ENST00000674294.1",
"protein_id": "ENSP00000501363.1",
"transcript_support_level": null,
"aa_start": 695,
"aa_end": null,
"aa_length": 707,
"cds_start": 2084,
"cds_end": null,
"cds_length": 2124,
"cdna_start": 2441,
"cdna_end": null,
"cdna_length": 2995,
"mane_select": "NM_001364171.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "TGPASST",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ODAD1",
"gene_hgnc_id": 26560,
"hgvs_c": "c.1956_1973dupCGGCCCTGCCTCCAGCAC",
"hgvs_p": "p.Thr658_Gly659insGlyProAlaSerSerThr",
"transcript": "ENST00000315396.7",
"protein_id": "ENSP00000318429.7",
"transcript_support_level": 1,
"aa_start": 658,
"aa_end": null,
"aa_length": 670,
"cds_start": 1973,
"cds_end": null,
"cds_length": 2013,
"cdna_start": 2656,
"cdna_end": null,
"cdna_length": 3215,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "TGPASST",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ODAD1",
"gene_hgnc_id": 26560,
"hgvs_c": "c.1956_1973dupCGGCCCTGCCTCCAGCAC",
"hgvs_p": "p.Thr658_Gly659insGlyProAlaSerSerThr",
"transcript": "NM_144577.4",
"protein_id": "NP_653178.3",
"transcript_support_level": null,
"aa_start": 658,
"aa_end": null,
"aa_length": 670,
"cds_start": 1973,
"cds_end": null,
"cds_length": 2013,
"cdna_start": 2080,
"cdna_end": null,
"cdna_length": 2644,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ODAD1",
"gene_hgnc_id": 26560,
"hgvs_c": "n.1502_1519dupCGGCCCTGCCTCCAGCAC",
"hgvs_p": null,
"transcript": "ENST00000497273.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2071,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ODAD1",
"gene_hgnc_id": 26560,
"hgvs_c": "n.*1672_*1689dupCGGCCCTGCCTCCAGCAC",
"hgvs_p": null,
"transcript": "ENST00000674207.1",
"protein_id": "ENSP00000501374.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3035,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ODAD1",
"gene_hgnc_id": 26560,
"hgvs_c": "c.*407_*424dupCGGCCCTGCCTCCAGCAC",
"hgvs_p": null,
"transcript": "ENST00000474199.6",
"protein_id": "ENSP00000501357.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 576,
"cds_start": -4,
"cds_end": null,
"cds_length": 1731,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2985,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ODAD1",
"gene_hgnc_id": 26560,
"hgvs_c": "n.*1672_*1689dupCGGCCCTGCCTCCAGCAC",
"hgvs_p": null,
"transcript": "ENST00000674207.1",
"protein_id": "ENSP00000501374.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3035,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ODAD1",
"gene_hgnc_id": 26560,
"dbsnp": "rs755466284",
"frequency_reference_population": 0.000114254915,
"hom_count_reference_population": 0,
"allele_count_reference_population": 184,
"gnomad_exomes_af": 0.000119318,
"gnomad_genomes_af": 0.0000657289,
"gnomad_exomes_ac": 174,
"gnomad_genomes_ac": 10,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 0.653,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM4",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001364171.2",
"gene_symbol": "ODAD1",
"hgnc_id": 26560,
"effects": [
"disruptive_inframe_insertion"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.2067_2084dupCGGCCCTGCCTCCAGCAC",
"hgvs_p": "p.Thr695_Gly696insGlyProAlaSerSerThr"
}
],
"clinvar_disease": "Primary ciliary dyskinesia",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Primary ciliary dyskinesia",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}