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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: 22-39022893-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=39022893&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 39022893,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_152426.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOBEC3D",
"gene_hgnc_id": 17354,
"hgvs_c": "c.89G>A",
"hgvs_p": "p.Arg30Gln",
"transcript": "NM_152426.4",
"protein_id": "NP_689639.2",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 386,
"cds_start": 89,
"cds_end": null,
"cds_length": 1161,
"cdna_start": 482,
"cdna_end": null,
"cdna_length": 2515,
"mane_select": "ENST00000216099.13",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_152426.4"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOBEC3D",
"gene_hgnc_id": 17354,
"hgvs_c": "c.89G>A",
"hgvs_p": "p.Arg30Gln",
"transcript": "ENST00000216099.13",
"protein_id": "ENSP00000216099.7",
"transcript_support_level": 2,
"aa_start": 30,
"aa_end": null,
"aa_length": 386,
"cds_start": 89,
"cds_end": null,
"cds_length": 1161,
"cdna_start": 482,
"cdna_end": null,
"cdna_length": 2515,
"mane_select": "NM_152426.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000216099.13"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000284554",
"gene_hgnc_id": null,
"hgvs_c": "c.89G>A",
"hgvs_p": "p.Arg30Gln",
"transcript": "ENST00000381568.9",
"protein_id": "ENSP00000370980.4",
"transcript_support_level": 1,
"aa_start": 30,
"aa_end": null,
"aa_length": 386,
"cds_start": 89,
"cds_end": null,
"cds_length": 1161,
"cdna_start": 89,
"cdna_end": null,
"cdna_length": 2121,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000381568.9"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOBEC3D",
"gene_hgnc_id": 17354,
"hgvs_c": "c.89G>A",
"hgvs_p": "p.Arg30Gln",
"transcript": "ENST00000427494.6",
"protein_id": "ENSP00000388017.2",
"transcript_support_level": 1,
"aa_start": 30,
"aa_end": null,
"aa_length": 202,
"cds_start": 89,
"cds_end": null,
"cds_length": 609,
"cdna_start": 496,
"cdna_end": null,
"cdna_length": 1961,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000427494.6"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOBEC3D",
"gene_hgnc_id": 17354,
"hgvs_c": "c.89G>A",
"hgvs_p": "p.Arg30Gln",
"transcript": "ENST00000951685.1",
"protein_id": "ENSP00000621744.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 303,
"cds_start": 89,
"cds_end": null,
"cds_length": 912,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 1565,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951685.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOBEC3D",
"gene_hgnc_id": 17354,
"hgvs_c": "c.89G>A",
"hgvs_p": "p.Arg30Gln",
"transcript": "ENST00000891546.1",
"protein_id": "ENSP00000561605.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 299,
"cds_start": 89,
"cds_end": null,
"cds_length": 900,
"cdna_start": 427,
"cdna_end": null,
"cdna_length": 2166,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000891546.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOBEC3D",
"gene_hgnc_id": 17354,
"hgvs_c": "c.89G>A",
"hgvs_p": "p.Arg30Gln",
"transcript": "NM_001363781.1",
"protein_id": "NP_001350710.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 202,
"cds_start": 89,
"cds_end": null,
"cds_length": 609,
"cdna_start": 482,
"cdna_end": null,
"cdna_length": 1937,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001363781.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOBEC3D",
"gene_hgnc_id": 17354,
"hgvs_c": "c.89G>A",
"hgvs_p": "p.Arg30Gln",
"transcript": "XM_017028596.3",
"protein_id": "XP_016884085.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 455,
"cds_start": 89,
"cds_end": null,
"cds_length": 1368,
"cdna_start": 482,
"cdna_end": null,
"cdna_length": 2722,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017028596.3"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOBEC3D",
"gene_hgnc_id": 17354,
"hgvs_c": "c.89G>A",
"hgvs_p": "p.Arg30Gln",
"transcript": "XM_047441142.1",
"protein_id": "XP_047297098.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 257,
"cds_start": 89,
"cds_end": null,
"cds_length": 774,
"cdna_start": 482,
"cdna_end": null,
"cdna_length": 1268,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047441142.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "APOBEC3D",
"gene_hgnc_id": 17354,
"hgvs_c": "c.17+1357G>A",
"hgvs_p": null,
"transcript": "ENST00000622217.3",
"protein_id": "ENSP00000480718.3",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 190,
"cds_start": null,
"cds_end": null,
"cds_length": 573,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 591,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000622217.3"
}
],
"gene_symbol": "APOBEC3D",
"gene_hgnc_id": 17354,
"dbsnp": "rs770105306",
"frequency_reference_population": 0.0000638435,
"hom_count_reference_population": 1,
"allele_count_reference_population": 103,
"gnomad_exomes_af": 0.0000663826,
"gnomad_genomes_af": 0.0000394493,
"gnomad_exomes_ac": 97,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.19415661692619324,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.359,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1419,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.26,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.084,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_152426.4",
"gene_symbol": "APOBEC3D",
"hgnc_id": 17354,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.89G>A",
"hgvs_p": "p.Arg30Gln"
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000381568.9",
"gene_symbol": "ENSG00000284554",
"hgnc_id": null,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.89G>A",
"hgvs_p": "p.Arg30Gln"
}
],
"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
}