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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: 6-51754962-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=51754962&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 51754962,
"ref": "T",
"alt": "C",
"effect": "intron_variant",
"transcript": "ENST00000371117.8",
"consequences": [
{
"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": 67,
"intron_rank": 55,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8643-24A>G",
"hgvs_p": null,
"transcript": "NM_138694.4",
"protein_id": "NP_619639.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 4074,
"cds_start": -4,
"cds_end": null,
"cds_length": 12225,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 16271,
"mane_select": "ENST00000371117.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": 55,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8643-24A>G",
"hgvs_p": null,
"transcript": "ENST00000371117.8",
"protein_id": "ENSP00000360158.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 4074,
"cds_start": -4,
"cds_end": null,
"cds_length": 12225,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 16271,
"mane_select": "NM_138694.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 56,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.*3002A>G",
"hgvs_p": null,
"transcript": "XM_047418895.1",
"protein_id": "XP_047274851.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2894,
"cds_start": -4,
"cds_end": null,
"cds_length": 8685,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13653,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 61,
"intron_rank": 55,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8643-24A>G",
"hgvs_p": null,
"transcript": "NM_170724.3",
"protein_id": "NP_733842.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3396,
"cds_start": -4,
"cds_end": null,
"cds_length": 10191,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11592,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 61,
"intron_rank": 55,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8643-24A>G",
"hgvs_p": null,
"transcript": "ENST00000340994.4",
"protein_id": "ENSP00000341097.4",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 3396,
"cds_start": -4,
"cds_end": null,
"cds_length": 10191,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11589,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": 55,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8643-24A>G",
"hgvs_p": null,
"transcript": "XM_011514680.4",
"protein_id": "XP_011512982.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 4074,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": 55,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8643-24A>G",
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"transcript": "XM_017010944.3",
"protein_id": "XP_016866433.1",
"transcript_support_level": null,
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"mane_select": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": 54,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8568-24A>G",
"hgvs_p": null,
"transcript": "XM_017010945.3",
"protein_id": "XP_016866434.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 4049,
"cds_start": -4,
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"cds_length": 12150,
"cdna_start": null,
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"cdna_length": 16196,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": 54,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8505-24A>G",
"hgvs_p": null,
"transcript": "XM_011514682.4",
"protein_id": "XP_011512984.1",
"transcript_support_level": null,
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},
{
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],
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"gene_symbol": "PKHD1",
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{
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],
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],
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],
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],
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": 55,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "n.8907-24A>G",
"hgvs_p": null,
"transcript": "XR_001743469.2",
"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": 11764,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"dbsnp": "rs2766125",
"frequency_reference_population": 0.015895274,
"hom_count_reference_population": 1565,
"allele_count_reference_population": 25438,
"gnomad_exomes_af": 0.0118813,
"gnomad_genomes_af": 0.0540896,
"gnomad_exomes_ac": 17206,
"gnomad_genomes_ac": 8232,
"gnomad_exomes_homalt": 911,
"gnomad_genomes_homalt": 654,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8500000238418579,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.85,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.401,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.05,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000371117.8",
"gene_symbol": "PKHD1",
"hgnc_id": 9016,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.8643-24A>G",
"hgvs_p": null
}
],
"clinvar_disease": "Autosomal recessive polycystic kidney disease,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not specified|not provided|Autosomal recessive polycystic kidney disease",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}