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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: 17-16940442-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=16940442&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 16940442,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000261652.7",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF13B",
"gene_hgnc_id": 18153,
"hgvs_c": "c.515G>A",
"hgvs_p": "p.Cys172Tyr",
"transcript": "NM_012452.3",
"protein_id": "NP_036584.1",
"transcript_support_level": null,
"aa_start": 172,
"aa_end": null,
"aa_length": 293,
"cds_start": 515,
"cds_end": null,
"cds_length": 882,
"cdna_start": 558,
"cdna_end": null,
"cdna_length": 1391,
"mane_select": "ENST00000261652.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF13B",
"gene_hgnc_id": 18153,
"hgvs_c": "c.515G>A",
"hgvs_p": "p.Cys172Tyr",
"transcript": "ENST00000261652.7",
"protein_id": "ENSP00000261652.2",
"transcript_support_level": 1,
"aa_start": 172,
"aa_end": null,
"aa_length": 293,
"cds_start": 515,
"cds_end": null,
"cds_length": 882,
"cdna_start": 558,
"cdna_end": null,
"cdna_length": 1391,
"mane_select": "NM_012452.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF13B",
"gene_hgnc_id": 18153,
"hgvs_c": "c.377G>A",
"hgvs_p": "p.Cys126Tyr",
"transcript": "ENST00000583789.1",
"protein_id": "ENSP00000462952.1",
"transcript_support_level": 1,
"aa_start": 126,
"aa_end": null,
"aa_length": 247,
"cds_start": 377,
"cds_end": null,
"cds_length": 744,
"cdna_start": 389,
"cdna_end": null,
"cdna_length": 859,
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF13B",
"gene_hgnc_id": 18153,
"hgvs_c": "n.621G>A",
"hgvs_p": null,
"transcript": "ENST00000579009.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 1978,
"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": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF13B",
"gene_hgnc_id": 18153,
"hgvs_c": "n.377G>A",
"hgvs_p": null,
"transcript": "ENST00000584950.5",
"protein_id": "ENSP00000463582.1",
"transcript_support_level": 5,
"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": 1266,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "TNFRSF13B",
"gene_hgnc_id": 18153,
"hgvs_c": "c.446-7266G>A",
"hgvs_p": null,
"transcript": "ENST00000579315.5",
"protein_id": "ENSP00000464069.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 156,
"cds_start": -4,
"cds_end": null,
"cds_length": 471,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 600,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TNFRSF13B",
"gene_hgnc_id": 18153,
"hgvs_c": "n.350-7505G>A",
"hgvs_p": null,
"transcript": "ENST00000582931.5",
"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": 554,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000307457",
"gene_hgnc_id": null,
"hgvs_c": "n.270+4098C>T",
"hgvs_p": null,
"transcript": "ENST00000826416.1",
"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": 465,
"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": "TNFRSF13B",
"gene_hgnc_id": 18153,
"hgvs_c": "n.*64G>A",
"hgvs_p": null,
"transcript": "ENST00000581616.2",
"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": 1420,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TNFRSF13B",
"gene_hgnc_id": 18153,
"dbsnp": "rs751216929",
"frequency_reference_population": 0.00017535554,
"hom_count_reference_population": 1,
"allele_count_reference_population": 283,
"gnomad_exomes_af": 0.000173773,
"gnomad_genomes_af": 0.000190554,
"gnomad_exomes_ac": 254,
"gnomad_genomes_ac": 29,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8719143271446228,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.71,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.5331,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.25,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.939,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate,BS1_Supporting",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate",
"BS1_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000261652.7",
"gene_symbol": "TNFRSF13B",
"hgnc_id": 18153,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.515G>A",
"hgvs_p": "p.Cys172Tyr"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000826416.1",
"gene_symbol": "ENSG00000307457",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.270+4098C>T",
"hgvs_p": null
}
],
"clinvar_disease": " 2, common variable,Immunodeficiency,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:6",
"phenotype_combined": "Immunodeficiency, common variable, 2|not provided|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}