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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: 8-109466593-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=109466593&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 109466593,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000378402.10",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 50,
"exon_rank_end": null,
"exon_count": 78,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1L1",
"gene_hgnc_id": 20313,
"hgvs_c": "c.8429C>A",
"hgvs_p": "p.Thr2810Asn",
"transcript": "NM_177531.6",
"protein_id": "NP_803875.2",
"transcript_support_level": null,
"aa_start": 2810,
"aa_end": null,
"aa_length": 4243,
"cds_start": 8429,
"cds_end": null,
"cds_length": 12732,
"cdna_start": 8549,
"cdna_end": null,
"cdna_length": 19969,
"mane_select": "ENST00000378402.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 50,
"exon_rank_end": null,
"exon_count": 78,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1L1",
"gene_hgnc_id": 20313,
"hgvs_c": "c.8429C>A",
"hgvs_p": "p.Thr2810Asn",
"transcript": "ENST00000378402.10",
"protein_id": "ENSP00000367655.5",
"transcript_support_level": 1,
"aa_start": 2810,
"aa_end": null,
"aa_length": 4243,
"cds_start": 8429,
"cds_end": null,
"cds_length": 12732,
"cdna_start": 8549,
"cdna_end": null,
"cdna_length": 19969,
"mane_select": "NM_177531.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 50,
"exon_rank_end": null,
"exon_count": 78,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1L1",
"gene_hgnc_id": 20313,
"hgvs_c": "c.8429C>A",
"hgvs_p": "p.Thr2810Asn",
"transcript": "XM_011517371.3",
"protein_id": "XP_011515673.1",
"transcript_support_level": null,
"aa_start": 2810,
"aa_end": null,
"aa_length": 4243,
"cds_start": 8429,
"cds_end": null,
"cds_length": 12732,
"cdna_start": 8549,
"cdna_end": null,
"cdna_length": 19415,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 77,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1L1",
"gene_hgnc_id": 20313,
"hgvs_c": "c.8315C>A",
"hgvs_p": "p.Thr2772Asn",
"transcript": "XM_047422420.1",
"protein_id": "XP_047278376.1",
"transcript_support_level": null,
"aa_start": 2772,
"aa_end": null,
"aa_length": 4205,
"cds_start": 8315,
"cds_end": null,
"cds_length": 12618,
"cdna_start": 8435,
"cdna_end": null,
"cdna_length": 19855,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 50,
"exon_rank_end": null,
"exon_count": 78,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1L1",
"gene_hgnc_id": 20313,
"hgvs_c": "c.8267C>A",
"hgvs_p": "p.Thr2756Asn",
"transcript": "XM_017013971.2",
"protein_id": "XP_016869460.2",
"transcript_support_level": null,
"aa_start": 2756,
"aa_end": null,
"aa_length": 4189,
"cds_start": 8267,
"cds_end": null,
"cds_length": 12570,
"cdna_start": 8387,
"cdna_end": null,
"cdna_length": 19807,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 48,
"exon_rank_end": null,
"exon_count": 76,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1L1",
"gene_hgnc_id": 20313,
"hgvs_c": "c.8126C>A",
"hgvs_p": "p.Thr2709Asn",
"transcript": "XM_047422421.1",
"protein_id": "XP_047278377.1",
"transcript_support_level": null,
"aa_start": 2709,
"aa_end": null,
"aa_length": 4142,
"cds_start": 8126,
"cds_end": null,
"cds_length": 12429,
"cdna_start": 8246,
"cdna_end": null,
"cdna_length": 19666,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1L1",
"gene_hgnc_id": 20313,
"hgvs_c": "c.5447C>A",
"hgvs_p": "p.Thr1816Asn",
"transcript": "XM_047422422.1",
"protein_id": "XP_047278378.1",
"transcript_support_level": null,
"aa_start": 1816,
"aa_end": null,
"aa_length": 3249,
"cds_start": 5447,
"cds_end": null,
"cds_length": 9750,
"cdna_start": 5546,
"cdna_end": null,
"cdna_length": 16966,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1L1",
"gene_hgnc_id": 20313,
"hgvs_c": "c.4805C>A",
"hgvs_p": "p.Thr1602Asn",
"transcript": "XM_017013974.2",
"protein_id": "XP_016869463.2",
"transcript_support_level": null,
"aa_start": 1602,
"aa_end": null,
"aa_length": 3035,
"cds_start": 4805,
"cds_end": null,
"cds_length": 9108,
"cdna_start": 5040,
"cdna_end": null,
"cdna_length": 16460,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PKHD1L1",
"gene_hgnc_id": 20313,
"dbsnp": "rs73313124",
"frequency_reference_population": 0.00051610253,
"hom_count_reference_population": 5,
"allele_count_reference_population": 824,
"gnomad_exomes_af": 0.000306696,
"gnomad_genomes_af": 0.00250401,
"gnomad_exomes_ac": 443,
"gnomad_genomes_ac": 381,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.008990943431854248,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.25,
"revel_prediction": "Benign",
"alphamissense_score": 0.1421,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.3,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.511,
"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,BS1,BS2",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000378402.10",
"gene_symbol": "PKHD1L1",
"hgnc_id": 20313,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.8429C>A",
"hgvs_p": "p.Thr2810Asn"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}