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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: 6-51659268-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=51659268&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 51659268,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000371117.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 61,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.10858C>T",
"hgvs_p": "p.Arg3620Cys",
"transcript": "NM_138694.4",
"protein_id": "NP_619639.3",
"transcript_support_level": null,
"aa_start": 3620,
"aa_end": null,
"aa_length": 4074,
"cds_start": 10858,
"cds_end": null,
"cds_length": 12225,
"cdna_start": 11122,
"cdna_end": null,
"cdna_length": 16271,
"mane_select": "ENST00000371117.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 61,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.10858C>T",
"hgvs_p": "p.Arg3620Cys",
"transcript": "ENST00000371117.8",
"protein_id": "ENSP00000360158.3",
"transcript_support_level": 1,
"aa_start": 3620,
"aa_end": null,
"aa_length": 4074,
"cds_start": 10858,
"cds_end": null,
"cds_length": 12225,
"cdna_start": 11122,
"cdna_end": null,
"cdna_length": 16271,
"mane_select": "NM_138694.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 61,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.10858C>T",
"hgvs_p": "p.Arg3620Cys",
"transcript": "XM_011514680.4",
"protein_id": "XP_011512982.1",
"transcript_support_level": null,
"aa_start": 3620,
"aa_end": null,
"aa_length": 4074,
"cds_start": 10858,
"cds_end": null,
"cds_length": 12225,
"cdna_start": 11481,
"cdna_end": null,
"cdna_length": 16630,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 61,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.10858C>T",
"hgvs_p": "p.Arg3620Cys",
"transcript": "XM_017010944.3",
"protein_id": "XP_016866433.1",
"transcript_support_level": null,
"aa_start": 3620,
"aa_end": null,
"aa_length": 4074,
"cds_start": 10858,
"cds_end": null,
"cds_length": 12225,
"cdna_start": 10960,
"cdna_end": null,
"cdna_length": 16109,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 60,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.10783C>T",
"hgvs_p": "p.Arg3595Cys",
"transcript": "XM_017010945.3",
"protein_id": "XP_016866434.1",
"transcript_support_level": null,
"aa_start": 3595,
"aa_end": null,
"aa_length": 4049,
"cds_start": 10783,
"cds_end": null,
"cds_length": 12150,
"cdna_start": 11047,
"cdna_end": null,
"cdna_length": 16196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 60,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.10720C>T",
"hgvs_p": "p.Arg3574Cys",
"transcript": "XM_011514682.4",
"protein_id": "XP_011512984.1",
"transcript_support_level": null,
"aa_start": 3574,
"aa_end": null,
"aa_length": 4028,
"cds_start": 10720,
"cds_end": null,
"cds_length": 12087,
"cdna_start": 10984,
"cdna_end": null,
"cdna_length": 16133,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 59,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.10663C>T",
"hgvs_p": "p.Arg3555Cys",
"transcript": "XM_017010946.3",
"protein_id": "XP_016866435.1",
"transcript_support_level": null,
"aa_start": 3555,
"aa_end": null,
"aa_length": 4009,
"cds_start": 10663,
"cds_end": null,
"cds_length": 12030,
"cdna_start": 10927,
"cdna_end": null,
"cdna_length": 16076,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 59,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.10594C>T",
"hgvs_p": "p.Arg3532Cys",
"transcript": "XM_017010947.3",
"protein_id": "XP_016866436.1",
"transcript_support_level": null,
"aa_start": 3532,
"aa_end": null,
"aa_length": 3986,
"cds_start": 10594,
"cds_end": null,
"cds_length": 11961,
"cdna_start": 10858,
"cdna_end": null,
"cdna_length": 16007,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 62,
"exon_rank_end": null,
"exon_count": 68,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.10216C>T",
"hgvs_p": "p.Arg3406Cys",
"transcript": "XM_011514683.4",
"protein_id": "XP_011512985.1",
"transcript_support_level": null,
"aa_start": 3406,
"aa_end": null,
"aa_length": 3860,
"cds_start": 10216,
"cds_end": null,
"cds_length": 11583,
"cdna_start": 10480,
"cdna_end": null,
"cdna_length": 15629,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 53,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.10147C>T",
"hgvs_p": "p.Arg3383Cys",
"transcript": "XM_011514684.4",
"protein_id": "XP_011512986.1",
"transcript_support_level": null,
"aa_start": 3383,
"aa_end": null,
"aa_length": 3837,
"cds_start": 10147,
"cds_end": null,
"cds_length": 11514,
"cdna_start": 10244,
"cdna_end": null,
"cdna_length": 15393,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 52,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.10147C>T",
"hgvs_p": "p.Arg3383Cys",
"transcript": "XM_017010948.3",
"protein_id": "XP_016866437.1",
"transcript_support_level": null,
"aa_start": 3383,
"aa_end": null,
"aa_length": 3837,
"cds_start": 10147,
"cds_end": null,
"cds_length": 11514,
"cdna_start": 10918,
"cdna_end": null,
"cdna_length": 16067,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8998C>T",
"hgvs_p": "p.Arg3000Cys",
"transcript": "XM_017010949.3",
"protein_id": "XP_016866438.1",
"transcript_support_level": null,
"aa_start": 3000,
"aa_end": null,
"aa_length": 3454,
"cds_start": 8998,
"cds_end": null,
"cds_length": 10365,
"cdna_start": 10097,
"cdna_end": null,
"cdna_length": 15246,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.4933C>T",
"hgvs_p": "p.Arg1645Cys",
"transcript": "XM_011514690.4",
"protein_id": "XP_011512992.1",
"transcript_support_level": null,
"aa_start": 1645,
"aa_end": null,
"aa_length": 2099,
"cds_start": 4933,
"cds_end": null,
"cds_length": 6300,
"cdna_start": 5020,
"cdna_end": null,
"cdna_length": 10169,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.4933C>T",
"hgvs_p": "p.Arg1645Cys",
"transcript": "XM_011514691.4",
"protein_id": "XP_011512993.1",
"transcript_support_level": null,
"aa_start": 1645,
"aa_end": null,
"aa_length": 2099,
"cds_start": 4933,
"cds_end": null,
"cds_length": 6300,
"cdna_start": 11042,
"cdna_end": null,
"cdna_length": 16191,
"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": 61,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "n.11122C>T",
"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
},
{
"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": 60,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.10157-10048C>T",
"hgvs_p": null,
"transcript": "XM_011514687.2",
"protein_id": "XP_011512989.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3395,
"cds_start": -4,
"cds_end": null,
"cds_length": 10188,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10547,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LOC124900615",
"gene_hgnc_id": null,
"hgvs_c": "n.155+6895G>A",
"hgvs_p": null,
"transcript": "XR_926871.3",
"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": 201,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"dbsnp": "rs557405366",
"frequency_reference_population": 0.000022929753,
"hom_count_reference_population": 0,
"allele_count_reference_population": 37,
"gnomad_exomes_af": 0.0000232632,
"gnomad_genomes_af": 0.0000197252,
"gnomad_exomes_ac": 34,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7291722297668457,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.471,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1756,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.1,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.919,
"phylop100way_prediction": "Uncertain_significance",
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000371117.8",
"gene_symbol": "PKHD1",
"hgnc_id": 9016,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.10858C>T",
"hgvs_p": "p.Arg3620Cys"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "XR_926871.3",
"gene_symbol": "LOC124900615",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.155+6895G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Autosomal recessive polycystic kidney disease,See cases,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "Autosomal recessive polycystic kidney disease|See cases|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}