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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: 19-50039240-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=50039240&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 50039240,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_015428.4",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF473",
"gene_hgnc_id": 23239,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Thr30Met",
"transcript": "NM_015428.4",
"protein_id": "NP_056243.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 871,
"cds_start": 89,
"cds_end": null,
"cds_length": 2616,
"cdna_start": 398,
"cdna_end": null,
"cdna_length": 4642,
"mane_select": "ENST00000270617.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF473",
"gene_hgnc_id": 23239,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Thr30Met",
"transcript": "ENST00000270617.8",
"protein_id": "ENSP00000270617.3",
"transcript_support_level": 1,
"aa_start": 30,
"aa_end": null,
"aa_length": 871,
"cds_start": 89,
"cds_end": null,
"cds_length": 2616,
"cdna_start": 398,
"cdna_end": null,
"cdna_length": 4642,
"mane_select": "NM_015428.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF473",
"gene_hgnc_id": 23239,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Thr30Met",
"transcript": "ENST00000391821.6",
"protein_id": "ENSP00000375697.1",
"transcript_support_level": 1,
"aa_start": 30,
"aa_end": null,
"aa_length": 871,
"cds_start": 89,
"cds_end": null,
"cds_length": 2616,
"cdna_start": 475,
"cdna_end": null,
"cdna_length": 4715,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF473",
"gene_hgnc_id": 23239,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Thr30Met",
"transcript": "NM_001006656.4",
"protein_id": "NP_001006657.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 871,
"cds_start": 89,
"cds_end": null,
"cds_length": 2616,
"cdna_start": 276,
"cdna_end": null,
"cdna_length": 4520,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF473",
"gene_hgnc_id": 23239,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Thr30Met",
"transcript": "ENST00000595661.5",
"protein_id": "ENSP00000472808.1",
"transcript_support_level": 5,
"aa_start": 30,
"aa_end": null,
"aa_length": 871,
"cds_start": 89,
"cds_end": null,
"cds_length": 2616,
"cdna_start": 584,
"cdna_end": null,
"cdna_length": 4828,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"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": "ZNF473",
"gene_hgnc_id": 23239,
"hgvs_c": "c.53C>T",
"hgvs_p": "p.Thr18Met",
"transcript": "NM_001308424.3",
"protein_id": "NP_001295353.1",
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 859,
"cds_start": 53,
"cds_end": null,
"cds_length": 2580,
"cdna_start": 198,
"cdna_end": null,
"cdna_length": 4442,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"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": "ZNF473",
"gene_hgnc_id": 23239,
"hgvs_c": "c.53C>T",
"hgvs_p": "p.Thr18Met",
"transcript": "ENST00000445728.7",
"protein_id": "ENSP00000388961.2",
"transcript_support_level": 2,
"aa_start": 18,
"aa_end": null,
"aa_length": 859,
"cds_start": 53,
"cds_end": null,
"cds_length": 2580,
"cdna_start": 198,
"cdna_end": null,
"cdna_length": 2833,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF473",
"gene_hgnc_id": 23239,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Thr30Met",
"transcript": "ENST00000599155.1",
"protein_id": "ENSP00000470862.1",
"transcript_support_level": 4,
"aa_start": 30,
"aa_end": null,
"aa_length": 101,
"cds_start": 89,
"cds_end": null,
"cds_length": 307,
"cdna_start": 340,
"cdna_end": null,
"cdna_length": 558,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF473",
"gene_hgnc_id": 23239,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Thr30Met",
"transcript": "ENST00000601364.5",
"protein_id": "ENSP00000471595.1",
"transcript_support_level": 3,
"aa_start": 30,
"aa_end": null,
"aa_length": 77,
"cds_start": 89,
"cds_end": null,
"cds_length": 234,
"cdna_start": 241,
"cdna_end": null,
"cdna_length": 603,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF473",
"gene_hgnc_id": 23239,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Thr30Met",
"transcript": "ENST00000598809.5",
"protein_id": "ENSP00000470956.1",
"transcript_support_level": 4,
"aa_start": 30,
"aa_end": null,
"aa_length": 73,
"cds_start": 89,
"cds_end": null,
"cds_length": 224,
"cdna_start": 470,
"cdna_end": null,
"cdna_length": 605,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF473",
"gene_hgnc_id": 23239,
"hgvs_c": "n.53C>T",
"hgvs_p": null,
"transcript": "ENST00000594968.1",
"protein_id": "ENSP00000472687.1",
"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": 475,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ZNF473",
"gene_hgnc_id": 23239,
"dbsnp": "rs371124736",
"frequency_reference_population": 0.00001363063,
"hom_count_reference_population": 0,
"allele_count_reference_population": 22,
"gnomad_exomes_af": 0.0000143656,
"gnomad_genomes_af": 0.00000657108,
"gnomad_exomes_ac": 21,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1438574194908142,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.135,
"revel_prediction": "Benign",
"alphamissense_score": 0.1898,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.63,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.577,
"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": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_015428.4",
"gene_symbol": "ZNF473",
"hgnc_id": 23239,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Thr30Met"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}