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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: 22-23573314-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=23573314&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 23573314,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_020070.4",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGLL1",
"gene_hgnc_id": 5870,
"hgvs_c": "c.594C>A",
"hgvs_p": "p.His198Gln",
"transcript": "NM_020070.4",
"protein_id": "NP_064455.1",
"transcript_support_level": null,
"aa_start": 198,
"aa_end": null,
"aa_length": 213,
"cds_start": 594,
"cds_end": null,
"cds_length": 642,
"cdna_start": 694,
"cdna_end": null,
"cdna_length": 883,
"mane_select": "ENST00000330377.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGLL1",
"gene_hgnc_id": 5870,
"hgvs_c": "c.594C>A",
"hgvs_p": "p.His198Gln",
"transcript": "ENST00000330377.3",
"protein_id": "ENSP00000329312.2",
"transcript_support_level": 1,
"aa_start": 198,
"aa_end": null,
"aa_length": 213,
"cds_start": 594,
"cds_end": null,
"cds_length": 642,
"cdna_start": 694,
"cdna_end": null,
"cdna_length": 883,
"mane_select": "NM_020070.4",
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGLL1",
"gene_hgnc_id": 5870,
"hgvs_c": "c.*223C>A",
"hgvs_p": null,
"transcript": "ENST00000249053.3",
"protein_id": "ENSP00000249053.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 84,
"cds_start": -4,
"cds_end": null,
"cds_length": 255,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 716,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGLL1",
"gene_hgnc_id": 5870,
"hgvs_c": "c.597C>A",
"hgvs_p": "p.His199Gln",
"transcript": "NM_001369906.1",
"protein_id": "NP_001356835.1",
"transcript_support_level": null,
"aa_start": 199,
"aa_end": null,
"aa_length": 214,
"cds_start": 597,
"cds_end": null,
"cds_length": 645,
"cdna_start": 697,
"cdna_end": null,
"cdna_length": 886,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGLL1",
"gene_hgnc_id": 5870,
"hgvs_c": "c.*223C>A",
"hgvs_p": null,
"transcript": "NM_152855.3",
"protein_id": "NP_690594.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 84,
"cds_start": -4,
"cds_end": null,
"cds_length": 255,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 767,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000224277",
"gene_hgnc_id": null,
"hgvs_c": "n.391-151G>T",
"hgvs_p": null,
"transcript": "ENST00000458318.2",
"protein_id": null,
"transcript_support_level": 3,
"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": 433,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGLL1",
"gene_hgnc_id": 5870,
"hgvs_c": "c.*55C>A",
"hgvs_p": null,
"transcript": "ENST00000438703.1",
"protein_id": "ENSP00000403391.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 179,
"cds_start": -4,
"cds_end": null,
"cds_length": 542,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 654,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000224277",
"gene_hgnc_id": null,
"hgvs_c": "n.*192G>T",
"hgvs_p": null,
"transcript": "ENST00000454863.4",
"protein_id": null,
"transcript_support_level": 4,
"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": 569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC105372957",
"gene_hgnc_id": null,
"hgvs_c": "n.*240G>T",
"hgvs_p": null,
"transcript": "XR_938075.2",
"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": 1299,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC105372957",
"gene_hgnc_id": null,
"hgvs_c": "n.*240G>T",
"hgvs_p": null,
"transcript": "XR_938076.1",
"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": 780,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC105372957",
"gene_hgnc_id": null,
"hgvs_c": "n.*216G>T",
"hgvs_p": null,
"transcript": "XR_938078.2",
"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": 1287,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "IGLL1",
"gene_hgnc_id": 5870,
"dbsnp": "rs1064418",
"frequency_reference_population": 0.00018907576,
"hom_count_reference_population": 0,
"allele_count_reference_population": 305,
"gnomad_exomes_af": 0.000192262,
"gnomad_genomes_af": 0.000158347,
"gnomad_exomes_ac": 281,
"gnomad_genomes_ac": 24,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8644041419029236,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.274,
"revel_prediction": "Benign",
"alphamissense_score": 0.739,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.37,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.122,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"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": "PP3_Moderate",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_020070.4",
"gene_symbol": "IGLL1",
"hgnc_id": 5870,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown,AR,AD",
"hgvs_c": "c.594C>A",
"hgvs_p": "p.His198Gln"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000458318.2",
"gene_symbol": "ENSG00000224277",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.391-151G>T",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "XR_938075.2",
"gene_symbol": "LOC105372957",
"hgnc_id": null,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*240G>T",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal recessive,Agammaglobulinemia 2,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "Agammaglobulinemia 2, autosomal recessive|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}