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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: 19-19563580-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=19563580&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 19563580,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_025245.3",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"hgvs_c": "c.961G>T",
"hgvs_p": "p.Asp321Tyr",
"transcript": "NM_025245.3",
"protein_id": "NP_079521.1",
"transcript_support_level": null,
"aa_start": 321,
"aa_end": null,
"aa_length": 374,
"cds_start": 961,
"cds_end": null,
"cds_length": 1125,
"cdna_start": 1019,
"cdna_end": null,
"cdna_length": 1495,
"mane_select": "ENST00000251203.14",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"hgvs_c": "c.961G>T",
"hgvs_p": "p.Asp321Tyr",
"transcript": "ENST00000251203.14",
"protein_id": "ENSP00000251203.5",
"transcript_support_level": 1,
"aa_start": 321,
"aa_end": null,
"aa_length": 374,
"cds_start": 961,
"cds_end": null,
"cds_length": 1125,
"cdna_start": 1019,
"cdna_end": null,
"cdna_length": 1495,
"mane_select": "NM_025245.3",
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"hgvs_c": "n.*519G>T",
"hgvs_p": null,
"transcript": "ENST00000557978.6",
"protein_id": "ENSP00000453348.1",
"transcript_support_level": 1,
"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": 1416,
"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": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"hgvs_c": "n.*519G>T",
"hgvs_p": null,
"transcript": "ENST00000557978.6",
"protein_id": "ENSP00000453348.1",
"transcript_support_level": 1,
"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": 1416,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"hgvs_c": "c.1012G>T",
"hgvs_p": "p.Asp338Tyr",
"transcript": "XM_011528320.4",
"protein_id": "XP_011526622.1",
"transcript_support_level": null,
"aa_start": 338,
"aa_end": null,
"aa_length": 391,
"cds_start": 1012,
"cds_end": null,
"cds_length": 1176,
"cdna_start": 1070,
"cdna_end": null,
"cdna_length": 1546,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"hgvs_c": "c.703G>T",
"hgvs_p": "p.Asp235Tyr",
"transcript": "XM_006722911.4",
"protein_id": "XP_006722974.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 288,
"cds_start": 703,
"cds_end": null,
"cds_length": 867,
"cdna_start": 983,
"cdna_end": null,
"cdna_length": 1459,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"hgvs_c": "c.703G>T",
"hgvs_p": "p.Asp235Tyr",
"transcript": "XM_011528322.2",
"protein_id": "XP_011526624.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 288,
"cds_start": 703,
"cds_end": null,
"cds_length": 867,
"cdna_start": 883,
"cdna_end": null,
"cdna_length": 1359,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"hgvs_c": "c.703G>T",
"hgvs_p": "p.Asp235Tyr",
"transcript": "XM_047439471.1",
"protein_id": "XP_047295427.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 288,
"cds_start": 703,
"cds_end": null,
"cds_length": 867,
"cdna_start": 945,
"cdna_end": null,
"cdna_length": 1421,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"hgvs_c": "c.466G>T",
"hgvs_p": "p.Asp156Tyr",
"transcript": "XM_017027329.3",
"protein_id": "XP_016882818.1",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 209,
"cds_start": 466,
"cds_end": null,
"cds_length": 630,
"cdna_start": 722,
"cdna_end": null,
"cdna_length": 1198,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"hgvs_c": "n.245G>T",
"hgvs_p": null,
"transcript": "ENST00000558276.7",
"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": 727,
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"hgvs_c": "n.918G>T",
"hgvs_p": null,
"transcript": "NR_038198.2",
"protein_id": null,
"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": 1394,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PBX4",
"gene_hgnc_id": 13403,
"dbsnp": null,
"frequency_reference_population": 0.0000014305476,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000143055,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6248251795768738,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.323,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1412,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.07,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.174,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
"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": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_025245.3",
"gene_symbol": "PBX4",
"hgnc_id": 13403,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.961G>T",
"hgvs_p": "p.Asp321Tyr"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}