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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: 8-144412594-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=144412594&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 144412594,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_130849.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A4",
"gene_hgnc_id": 17129,
"hgvs_c": "c.1888G>C",
"hgvs_p": "p.Gly630Arg",
"transcript": "NM_130849.4",
"protein_id": "NP_570901.3",
"transcript_support_level": null,
"aa_start": 630,
"aa_end": null,
"aa_length": 647,
"cds_start": 1888,
"cds_end": null,
"cds_length": 1944,
"cdna_start": 1943,
"cdna_end": null,
"cdna_length": 2123,
"mane_select": "ENST00000301305.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A4",
"gene_hgnc_id": 17129,
"hgvs_c": "c.1888G>C",
"hgvs_p": "p.Gly630Arg",
"transcript": "ENST00000301305.8",
"protein_id": "ENSP00000301305.4",
"transcript_support_level": 1,
"aa_start": 630,
"aa_end": null,
"aa_length": 647,
"cds_start": 1888,
"cds_end": null,
"cds_length": 1944,
"cdna_start": 1943,
"cdna_end": null,
"cdna_length": 2123,
"mane_select": "NM_130849.4",
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A4",
"gene_hgnc_id": 17129,
"hgvs_c": "n.488G>C",
"hgvs_p": null,
"transcript": "ENST00000532718.5",
"protein_id": null,
"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": 668,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A4",
"gene_hgnc_id": 17129,
"hgvs_c": "c.1813G>C",
"hgvs_p": "p.Gly605Arg",
"transcript": "NM_017767.3",
"protein_id": "NP_060237.3",
"transcript_support_level": null,
"aa_start": 605,
"aa_end": null,
"aa_length": 622,
"cds_start": 1813,
"cds_end": null,
"cds_length": 1869,
"cdna_start": 2054,
"cdna_end": null,
"cdna_length": 2234,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A4",
"gene_hgnc_id": 17129,
"hgvs_c": "c.1813G>C",
"hgvs_p": "p.Gly605Arg",
"transcript": "ENST00000276833.9",
"protein_id": "ENSP00000276833.5",
"transcript_support_level": 2,
"aa_start": 605,
"aa_end": null,
"aa_length": 622,
"cds_start": 1813,
"cds_end": null,
"cds_length": 1869,
"cdna_start": 2117,
"cdna_end": null,
"cdna_length": 2297,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A4",
"gene_hgnc_id": 17129,
"hgvs_c": "c.1606G>C",
"hgvs_p": "p.Gly536Arg",
"transcript": "NM_001374839.1",
"protein_id": "NP_001361768.1",
"transcript_support_level": null,
"aa_start": 536,
"aa_end": null,
"aa_length": 553,
"cds_start": 1606,
"cds_end": null,
"cds_length": 1662,
"cdna_start": 1661,
"cdna_end": null,
"cdna_length": 1841,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A4",
"gene_hgnc_id": 17129,
"hgvs_c": "c.394G>C",
"hgvs_p": "p.Gly132Arg",
"transcript": "NM_001280557.2",
"protein_id": "NP_001267486.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 149,
"cds_start": 394,
"cds_end": null,
"cds_length": 450,
"cdna_start": 487,
"cdna_end": null,
"cdna_length": 667,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A4",
"gene_hgnc_id": 17129,
"hgvs_c": "c.1453G>C",
"hgvs_p": "p.Gly485Arg",
"transcript": "XM_024447189.2",
"protein_id": "XP_024302957.1",
"transcript_support_level": null,
"aa_start": 485,
"aa_end": null,
"aa_length": 502,
"cds_start": 1453,
"cds_end": null,
"cds_length": 1509,
"cdna_start": 1508,
"cdna_end": null,
"cdna_length": 1688,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A4",
"gene_hgnc_id": 17129,
"hgvs_c": "n.473G>C",
"hgvs_p": null,
"transcript": "ENST00000527148.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 684,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A4",
"gene_hgnc_id": 17129,
"hgvs_c": "n.579G>C",
"hgvs_p": null,
"transcript": "ENST00000529462.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 2778,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A4",
"gene_hgnc_id": 17129,
"hgvs_c": "n.318G>C",
"hgvs_p": null,
"transcript": "ENST00000530807.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 498,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A4",
"gene_hgnc_id": 17129,
"hgvs_c": "n.616G>C",
"hgvs_p": null,
"transcript": "ENST00000531013.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 795,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC39A4",
"gene_hgnc_id": 17129,
"dbsnp": "rs1554871810",
"frequency_reference_population": 6.8405444e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84054e-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": 0.9080135822296143,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.288,
"revel_prediction": "Benign",
"alphamissense_score": 0.8891,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.08,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": -1.28,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Moderate,PP5_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_130849.4",
"gene_symbol": "SLC39A4",
"hgnc_id": 17129,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1888G>C",
"hgvs_p": "p.Gly630Arg"
}
],
"clinvar_disease": "Hereditary acrodermatitis enteropathica",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Hereditary acrodermatitis enteropathica",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}