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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: 19-2733163-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=2733163&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SLC39A3",
"hgnc_id": 17128,
"hgvs_c": "c.533C>T",
"hgvs_p": "p.Ser178Leu",
"inheritance_mode": "AR",
"pathogenic_score": 3,
"score": 3,
"transcript": "NM_144564.5",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000267001",
"hgnc_id": null,
"hgvs_c": "c.210+3885C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 3,
"score": 3,
"transcript": "ENST00000586572.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_score": 3,
"allele_count_reference_population": 8,
"alphamissense_prediction": null,
"alphamissense_score": 0.3584,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.12,
"chr": "19",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.801226019859314,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 314,
"aa_ref": "S",
"aa_start": 178,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1367,
"cdna_start": 728,
"cds_end": null,
"cds_length": 945,
"cds_start": 533,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_144564.5",
"gene_hgnc_id": 17128,
"gene_symbol": "SLC39A3",
"hgvs_c": "c.533C>T",
"hgvs_p": "p.Ser178Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000269740.9",
"protein_coding": true,
"protein_id": "NP_653165.2",
"strand": false,
"transcript": "NM_144564.5",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 314,
"aa_ref": "S",
"aa_start": 178,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1367,
"cdna_start": 728,
"cds_end": null,
"cds_length": 945,
"cds_start": 533,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000269740.9",
"gene_hgnc_id": 17128,
"gene_symbol": "SLC39A3",
"hgvs_c": "c.533C>T",
"hgvs_p": "p.Ser178Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_144564.5",
"protein_coding": true,
"protein_id": "ENSP00000269740.3",
"strand": false,
"transcript": "ENST00000269740.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 104,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 543,
"cdna_start": null,
"cds_end": null,
"cds_length": 317,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000586572.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000267001",
"hgvs_c": "c.210+3885C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000467958.1",
"strand": false,
"transcript": "ENST00000586572.1",
"transcript_support_level": 4
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 323,
"aa_ref": "S",
"aa_start": 178,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1219,
"cdna_start": 728,
"cds_end": null,
"cds_length": 972,
"cds_start": 533,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000545664.5",
"gene_hgnc_id": 17128,
"gene_symbol": "SLC39A3",
"hgvs_c": "c.533C>T",
"hgvs_p": "p.Ser178Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000445345.1",
"strand": false,
"transcript": "ENST00000545664.5",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 314,
"aa_ref": "S",
"aa_start": 178,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1523,
"cdna_start": 884,
"cds_end": null,
"cds_length": 945,
"cds_start": 533,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000909979.1",
"gene_hgnc_id": 17128,
"gene_symbol": "SLC39A3",
"hgvs_c": "c.533C>T",
"hgvs_p": "p.Ser178Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580038.1",
"strand": false,
"transcript": "ENST00000909979.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 314,
"aa_ref": "S",
"aa_start": 178,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1418,
"cdna_start": 781,
"cds_end": null,
"cds_length": 945,
"cds_start": 533,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000909980.1",
"gene_hgnc_id": 17128,
"gene_symbol": "SLC39A3",
"hgvs_c": "c.533C>T",
"hgvs_p": "p.Ser178Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580039.1",
"strand": false,
"transcript": "ENST00000909980.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 314,
"aa_ref": "S",
"aa_start": 178,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1301,
"cdna_start": 662,
"cds_end": null,
"cds_length": 945,
"cds_start": 533,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000909981.1",
"gene_hgnc_id": 17128,
"gene_symbol": "SLC39A3",
"hgvs_c": "c.533C>T",
"hgvs_p": "p.Ser178Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580040.1",
"strand": false,
"transcript": "ENST00000909981.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 314,
"aa_ref": "S",
"aa_start": 178,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1768,
"cdna_start": 1129,
"cds_end": null,
"cds_length": 945,
"cds_start": 533,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000909982.1",
"gene_hgnc_id": 17128,
"gene_symbol": "SLC39A3",
"hgvs_c": "c.533C>T",
"hgvs_p": "p.Ser178Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580041.1",
"strand": false,
"transcript": "ENST00000909982.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 314,
"aa_ref": "S",
"aa_start": 178,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1331,
"cdna_start": 701,
"cds_end": null,
"cds_length": 945,
"cds_start": 533,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000959861.1",
"gene_hgnc_id": 17128,
"gene_symbol": "SLC39A3",
"hgvs_c": "c.533C>T",
"hgvs_p": "p.Ser178Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629920.1",
"strand": false,
"transcript": "ENST00000959861.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 314,
"aa_ref": "S",
"aa_start": 178,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1431,
"cdna_start": 797,
"cds_end": null,
"cds_length": 945,
"cds_start": 533,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000959862.1",
"gene_hgnc_id": 17128,
"gene_symbol": "SLC39A3",
"hgvs_c": "c.533C>T",
"hgvs_p": "p.Ser178Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629921.1",
"strand": false,
"transcript": "ENST00000959862.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 314,
"aa_ref": "S",
"aa_start": 178,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1456,
"cdna_start": 834,
"cds_end": null,
"cds_length": 945,
"cds_start": 533,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000959863.1",
"gene_hgnc_id": 17128,
"gene_symbol": "SLC39A3",
"hgvs_c": "c.533C>T",
"hgvs_p": "p.Ser178Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629922.1",
"strand": false,
"transcript": "ENST00000959863.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 312,
"aa_ref": "S",
"aa_start": 176,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1332,
"cdna_start": 693,
"cds_end": null,
"cds_length": 939,
"cds_start": 527,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000909983.1",
"gene_hgnc_id": 17128,
"gene_symbol": "SLC39A3",
"hgvs_c": "c.527C>T",
"hgvs_p": "p.Ser176Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580042.1",
"strand": false,
"transcript": "ENST00000909983.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 135,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 524,
"cdna_start": null,
"cds_end": null,
"cds_length": 408,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000589363.5",
"gene_hgnc_id": 17128,
"gene_symbol": "SLC39A3",
"hgvs_c": "c.*125C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000465383.1",
"strand": true,
"transcript": "ENST00000589363.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 106,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 491,
"cdna_start": null,
"cds_end": null,
"cds_length": 323,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000589166.1",
"gene_hgnc_id": 17128,
"gene_symbol": "SLC39A3",
"hgvs_c": "c.*210C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000466969.1",
"strand": true,
"transcript": "ENST00000589166.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs572760698",
"effect": "missense_variant",
"frequency_reference_population": 0.0000054862157,
"gene_hgnc_id": 17128,
"gene_symbol": "SLC39A3",
"gnomad_exomes_ac": 8,
"gnomad_exomes_af": 0.00000548622,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.013,
"pos": 2733163,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.33,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_144564.5"
}
]
}