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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: 12-57742040-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=57742040&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 57742040,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_014770.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP2",
"gene_hgnc_id": 16921,
"hgvs_c": "c.32C>T",
"hgvs_p": "p.Ala11Val",
"transcript": "ENST00000257897.7",
"protein_id": "ENSP00000257897.3",
"transcript_support_level": 1,
"aa_start": 11,
"aa_end": null,
"aa_length": 836,
"cds_start": 32,
"cds_end": null,
"cds_length": 2511,
"cdna_start": 118,
"cdna_end": null,
"cdna_length": 5388,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP2",
"gene_hgnc_id": 16921,
"hgvs_c": "c.32C>T",
"hgvs_p": "p.Ala11Val",
"transcript": "NM_014770.4",
"protein_id": "NP_055585.1",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 836,
"cds_start": 32,
"cds_end": null,
"cds_length": 2511,
"cdna_start": 122,
"cdna_end": null,
"cdna_length": 5392,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP2",
"gene_hgnc_id": 16921,
"hgvs_c": "c.32C>T",
"hgvs_p": "p.Ala11Val",
"transcript": "XM_005268626.3",
"protein_id": "XP_005268683.1",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 856,
"cds_start": 32,
"cds_end": null,
"cds_length": 2571,
"cdna_start": 122,
"cdna_end": null,
"cdna_length": 5452,
"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": 1,
"intron_rank_end": null,
"gene_symbol": "TSPAN31",
"gene_hgnc_id": 10539,
"hgvs_c": "n.235+2070G>A",
"hgvs_p": null,
"transcript": "ENST00000547311.5",
"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": 438,
"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": 1,
"intron_rank_end": null,
"gene_symbol": "TSPAN31",
"gene_hgnc_id": 10539,
"hgvs_c": "n.105+2070G>A",
"hgvs_p": null,
"transcript": "ENST00000550528.5",
"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": 534,
"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": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TSPAN31",
"gene_hgnc_id": 10539,
"hgvs_c": "n.190-1200G>A",
"hgvs_p": null,
"transcript": "ENST00000553221.5",
"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": 675,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "AGAP2",
"gene_hgnc_id": 16921,
"dbsnp": "rs201928942",
"frequency_reference_population": 0.00060529535,
"hom_count_reference_population": 11,
"allele_count_reference_population": 977,
"gnomad_exomes_af": 0.000640288,
"gnomad_genomes_af": 0.000269301,
"gnomad_exomes_ac": 936,
"gnomad_genomes_ac": 41,
"gnomad_exomes_homalt": 11,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.009385824203491211,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.102,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.45,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.998,
"phylop100way_prediction": "Uncertain_significance",
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_014770.4",
"gene_symbol": "AGAP2",
"hgnc_id": 16921,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.32C>T",
"hgvs_p": "p.Ala11Val"
},
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000547311.5",
"gene_symbol": "TSPAN31",
"hgnc_id": 10539,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.235+2070G>A",
"hgvs_p": null
}
],
"clinvar_disease": "AGAP2-related disorder",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "AGAP2-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}