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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: 4-25362279-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=25362279&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 25362279,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000302874.9",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZCCHC4",
"gene_hgnc_id": 22917,
"hgvs_c": "c.1187T>A",
"hgvs_p": "p.Leu396His",
"transcript": "NM_024936.3",
"protein_id": "NP_079212.2",
"transcript_support_level": null,
"aa_start": 396,
"aa_end": null,
"aa_length": 513,
"cds_start": 1187,
"cds_end": null,
"cds_length": 1542,
"cdna_start": 1223,
"cdna_end": null,
"cdna_length": 2797,
"mane_select": "ENST00000302874.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZCCHC4",
"gene_hgnc_id": 22917,
"hgvs_c": "c.1187T>A",
"hgvs_p": "p.Leu396His",
"transcript": "ENST00000302874.9",
"protein_id": "ENSP00000303468.4",
"transcript_support_level": 1,
"aa_start": 396,
"aa_end": null,
"aa_length": 513,
"cds_start": 1187,
"cds_end": null,
"cds_length": 1542,
"cdna_start": 1223,
"cdna_end": null,
"cdna_length": 2797,
"mane_select": "NM_024936.3",
"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": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZCCHC4",
"gene_hgnc_id": 22917,
"hgvs_c": "n.*172T>A",
"hgvs_p": null,
"transcript": "ENST00000507760.5",
"protein_id": "ENSP00000422115.1",
"transcript_support_level": 1,
"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": 2045,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZCCHC4",
"gene_hgnc_id": 22917,
"hgvs_c": "n.*172T>A",
"hgvs_p": null,
"transcript": "ENST00000507760.5",
"protein_id": "ENSP00000422115.1",
"transcript_support_level": 1,
"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": 2045,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZCCHC4",
"gene_hgnc_id": 22917,
"hgvs_c": "c.779T>A",
"hgvs_p": "p.Leu260His",
"transcript": "ENST00000505412.1",
"protein_id": "ENSP00000422269.1",
"transcript_support_level": 3,
"aa_start": 260,
"aa_end": null,
"aa_length": 301,
"cds_start": 779,
"cds_end": null,
"cds_length": 906,
"cdna_start": 780,
"cdna_end": null,
"cdna_length": 1903,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZCCHC4",
"gene_hgnc_id": 22917,
"hgvs_c": "c.1232T>A",
"hgvs_p": "p.Leu411His",
"transcript": "XM_011513835.3",
"protein_id": "XP_011512137.1",
"transcript_support_level": null,
"aa_start": 411,
"aa_end": null,
"aa_length": 528,
"cds_start": 1232,
"cds_end": null,
"cds_length": 1587,
"cdna_start": 1268,
"cdna_end": null,
"cdna_length": 2842,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZCCHC4",
"gene_hgnc_id": 22917,
"hgvs_c": "c.935T>A",
"hgvs_p": "p.Leu312His",
"transcript": "XM_017008129.3",
"protein_id": "XP_016863618.1",
"transcript_support_level": null,
"aa_start": 312,
"aa_end": null,
"aa_length": 429,
"cds_start": 935,
"cds_end": null,
"cds_length": 1290,
"cdna_start": 971,
"cdna_end": null,
"cdna_length": 2545,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZCCHC4",
"gene_hgnc_id": 22917,
"hgvs_c": "n.326T>A",
"hgvs_p": null,
"transcript": "ENST00000508058.1",
"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": 527,
"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": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZCCHC4",
"gene_hgnc_id": 22917,
"hgvs_c": "n.1268T>A",
"hgvs_p": null,
"transcript": "XR_925324.4",
"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": 3074,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ZCCHC4",
"gene_hgnc_id": 22917,
"dbsnp": "rs315675",
"frequency_reference_population": 0.89101034,
"hom_count_reference_population": 638947,
"allele_count_reference_population": 1431458,
"gnomad_exomes_af": 0.88939,
"gnomad_genomes_af": 0.906484,
"gnomad_exomes_ac": 1293415,
"gnomad_genomes_ac": 138043,
"gnomad_exomes_homalt": 576146,
"gnomad_genomes_homalt": 62801,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.000002560734401413356,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.074,
"revel_prediction": "Benign",
"alphamissense_score": 0.0522,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.868,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000302874.9",
"gene_symbol": "ZCCHC4",
"hgnc_id": 22917,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1187T>A",
"hgvs_p": "p.Leu396His"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}