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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: 5-41842690-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=41842690&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 41842690,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000196371.10",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXCT1",
"gene_hgnc_id": 8527,
"hgvs_c": "c.656G>A",
"hgvs_p": "p.Gly219Glu",
"transcript": "NM_000436.4",
"protein_id": "NP_000427.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 520,
"cds_start": 656,
"cds_end": null,
"cds_length": 1563,
"cdna_start": 723,
"cdna_end": null,
"cdna_length": 3294,
"mane_select": "ENST00000196371.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXCT1",
"gene_hgnc_id": 8527,
"hgvs_c": "c.656G>A",
"hgvs_p": "p.Gly219Glu",
"transcript": "ENST00000196371.10",
"protein_id": "ENSP00000196371.5",
"transcript_support_level": 1,
"aa_start": 219,
"aa_end": null,
"aa_length": 520,
"cds_start": 656,
"cds_end": null,
"cds_length": 1563,
"cdna_start": 723,
"cdna_end": null,
"cdna_length": 3294,
"mane_select": "NM_000436.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXCT1",
"gene_hgnc_id": 8527,
"hgvs_c": "c.677G>A",
"hgvs_p": "p.Gly226Glu",
"transcript": "NM_001364299.2",
"protein_id": "NP_001351228.1",
"transcript_support_level": null,
"aa_start": 226,
"aa_end": null,
"aa_length": 527,
"cds_start": 677,
"cds_end": null,
"cds_length": 1584,
"cdna_start": 744,
"cdna_end": null,
"cdna_length": 3315,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXCT1",
"gene_hgnc_id": 8527,
"hgvs_c": "c.677G>A",
"hgvs_p": "p.Gly226Glu",
"transcript": "NM_001364300.2",
"protein_id": "NP_001351229.1",
"transcript_support_level": null,
"aa_start": 226,
"aa_end": null,
"aa_length": 527,
"cds_start": 677,
"cds_end": null,
"cds_length": 1584,
"cdna_start": 1359,
"cdna_end": null,
"cdna_length": 3930,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXCT1",
"gene_hgnc_id": 8527,
"hgvs_c": "c.656G>A",
"hgvs_p": "p.Gly219Glu",
"transcript": "NM_001364301.2",
"protein_id": "NP_001351230.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 518,
"cds_start": 656,
"cds_end": null,
"cds_length": 1557,
"cdna_start": 723,
"cdna_end": null,
"cdna_length": 3288,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXCT1",
"gene_hgnc_id": 8527,
"hgvs_c": "c.656G>A",
"hgvs_p": "p.Gly219Glu",
"transcript": "NM_001364302.2",
"protein_id": "NP_001351231.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 490,
"cds_start": 656,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 723,
"cdna_end": null,
"cdna_length": 3204,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXCT1",
"gene_hgnc_id": 8527,
"hgvs_c": "c.98G>A",
"hgvs_p": "p.Gly33Glu",
"transcript": "NM_001364303.2",
"protein_id": "NP_001351232.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 334,
"cds_start": 98,
"cds_end": null,
"cds_length": 1005,
"cdna_start": 175,
"cdna_end": null,
"cdna_length": 2746,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXCT1",
"gene_hgnc_id": 8527,
"hgvs_c": "c.98G>A",
"hgvs_p": "p.Gly33Glu",
"transcript": "ENST00000509987.1",
"protein_id": "ENSP00000425348.1",
"transcript_support_level": 2,
"aa_start": 33,
"aa_end": null,
"aa_length": 334,
"cds_start": 98,
"cds_end": null,
"cds_length": 1005,
"cdna_start": 175,
"cdna_end": null,
"cdna_length": 1441,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXCT1",
"gene_hgnc_id": 8527,
"hgvs_c": "n.68G>A",
"hgvs_p": null,
"transcript": "ENST00000514723.1",
"protein_id": null,
"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": 241,
"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": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXCT1",
"gene_hgnc_id": 8527,
"hgvs_c": "n.723G>A",
"hgvs_p": null,
"transcript": "NR_157114.2",
"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": 3221,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "OXCT1",
"gene_hgnc_id": 8527,
"dbsnp": "rs121909302",
"frequency_reference_population": 6.849672e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84967e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.992010235786438,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.97,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9715,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.59,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.754,
"phylop100way_prediction": "Pathogenic",
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000196371.10",
"gene_symbol": "OXCT1",
"hgnc_id": 8527,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.656G>A",
"hgvs_p": "p.Gly219Glu"
}
],
"clinvar_disease": "Succinyl-CoA acetoacetate transferase deficiency",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Succinyl-CoA acetoacetate transferase deficiency",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}