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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: 19-56384127-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=56384127&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 56384127,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_144690.3",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF582",
"gene_hgnc_id": 26421,
"hgvs_c": "c.1290G>A",
"hgvs_p": "p.Lys430Lys",
"transcript": "NM_001320371.4",
"protein_id": "NP_001307300.2",
"transcript_support_level": null,
"aa_start": 430,
"aa_end": null,
"aa_length": 517,
"cds_start": 1290,
"cds_end": null,
"cds_length": 1554,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000586929.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001320371.4"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF582",
"gene_hgnc_id": 26421,
"hgvs_c": "c.1290G>A",
"hgvs_p": "p.Lys430Lys",
"transcript": "ENST00000586929.6",
"protein_id": "ENSP00000465619.1",
"transcript_support_level": 1,
"aa_start": 430,
"aa_end": null,
"aa_length": 517,
"cds_start": 1290,
"cds_end": null,
"cds_length": 1554,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001320371.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000586929.6"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF582",
"gene_hgnc_id": 26421,
"hgvs_c": "c.1290G>A",
"hgvs_p": "p.Lys430Lys",
"transcript": "ENST00000301310.8",
"protein_id": "ENSP00000301310.3",
"transcript_support_level": 1,
"aa_start": 430,
"aa_end": null,
"aa_length": 517,
"cds_start": 1290,
"cds_end": null,
"cds_length": 1554,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000301310.8"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF582",
"gene_hgnc_id": 26421,
"hgvs_c": "c.1290G>A",
"hgvs_p": "p.Lys430Lys",
"transcript": "NM_144690.3",
"protein_id": "NP_653291.1",
"transcript_support_level": null,
"aa_start": 430,
"aa_end": null,
"aa_length": 517,
"cds_start": 1290,
"cds_end": null,
"cds_length": 1554,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_144690.3"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF582",
"gene_hgnc_id": 26421,
"hgvs_c": "c.1290G>A",
"hgvs_p": "p.Lys430Lys",
"transcript": "ENST00000932869.1",
"protein_id": "ENSP00000602928.1",
"transcript_support_level": null,
"aa_start": 430,
"aa_end": null,
"aa_length": 517,
"cds_start": 1290,
"cds_end": null,
"cds_length": 1554,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932869.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ZNF582",
"gene_hgnc_id": 26421,
"hgvs_c": "c.232+5874G>A",
"hgvs_p": null,
"transcript": "ENST00000589143.5",
"protein_id": "ENSP00000468679.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 102,
"cds_start": null,
"cds_end": null,
"cds_length": 310,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000589143.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ZNF582",
"gene_hgnc_id": 26421,
"hgvs_c": "c.232+5874G>A",
"hgvs_p": null,
"transcript": "ENST00000589895.2",
"protein_id": "ENSP00000465639.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 77,
"cds_start": null,
"cds_end": null,
"cds_length": 235,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000589895.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF582",
"gene_hgnc_id": 26421,
"hgvs_c": "n.1463G>A",
"hgvs_p": null,
"transcript": "XR_007066621.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007066621.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF582",
"gene_hgnc_id": 26421,
"hgvs_c": "n.1685G>A",
"hgvs_p": null,
"transcript": "XR_430188.4",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_430188.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285996",
"gene_hgnc_id": null,
"hgvs_c": "n.*203C>T",
"hgvs_p": null,
"transcript": "ENST00000651165.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000651165.1"
}
],
"gene_symbol": "ZNF582",
"gene_hgnc_id": 26421,
"dbsnp": "rs12978696",
"frequency_reference_population": 0.13266714,
"hom_count_reference_population": 15257,
"allele_count_reference_population": 213904,
"gnomad_exomes_af": 0.133274,
"gnomad_genomes_af": 0.126842,
"gnomad_exomes_ac": 194605,
"gnomad_genomes_ac": 19299,
"gnomad_exomes_homalt": 13943,
"gnomad_genomes_homalt": 1314,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6000000238418579,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.6,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.519,
"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": -14,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BP7,BA1",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_144690.3",
"gene_symbol": "ZNF582",
"hgnc_id": 26421,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1290G>A",
"hgvs_p": "p.Lys430Lys"
},
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000651165.1",
"gene_symbol": "ENSG00000285996",
"hgnc_id": null,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*203C>T",
"hgvs_p": null
}
],
"clinvar_disease": "ZNF582-related disorder",
"clinvar_classification": "Benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "ZNF582-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}