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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: 6-51619106-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=51619106&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PKHD1",
"hgnc_id": 9016,
"hgvs_c": "c.12200C>T",
"hgvs_p": "p.Pro4067Leu",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_138694.4",
"verdict": "Uncertain_significance"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000228689",
"hgnc_id": null,
"hgvs_c": "n.81-3249G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "ENST00000454361.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 25,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0838,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.33,
"chr": "6",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Autosomal recessive polycystic kidney disease,Polycystic kidney disease 4,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.08420124650001526,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 4074,
"aa_ref": "P",
"aa_start": 4067,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 16271,
"cdna_start": 12464,
"cds_end": null,
"cds_length": 12225,
"cds_start": 12200,
"consequences": [
"missense_variant"
],
"exon_count": 67,
"exon_rank": 67,
"exon_rank_end": null,
"feature": "NM_138694.4",
"gene_hgnc_id": 9016,
"gene_symbol": "PKHD1",
"hgvs_c": "c.12200C>T",
"hgvs_p": "p.Pro4067Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000371117.8",
"protein_coding": true,
"protein_id": "NP_619639.3",
"strand": false,
"transcript": "NM_138694.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 4074,
"aa_ref": "P",
"aa_start": 4067,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 16271,
"cdna_start": 12464,
"cds_end": null,
"cds_length": 12225,
"cds_start": 12200,
"consequences": [
"missense_variant"
],
"exon_count": 67,
"exon_rank": 67,
"exon_rank_end": null,
"feature": "ENST00000371117.8",
"gene_hgnc_id": 9016,
"gene_symbol": "PKHD1",
"hgvs_c": "c.12200C>T",
"hgvs_p": "p.Pro4067Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_138694.4",
"protein_coding": true,
"protein_id": "ENSP00000360158.3",
"strand": false,
"transcript": "ENST00000371117.8",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 4074,
"aa_ref": "P",
"aa_start": 4067,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 16630,
"cdna_start": 12823,
"cds_end": null,
"cds_length": 12225,
"cds_start": 12200,
"consequences": [
"missense_variant"
],
"exon_count": 67,
"exon_rank": 67,
"exon_rank_end": null,
"feature": "XM_011514680.4",
"gene_hgnc_id": 9016,
"gene_symbol": "PKHD1",
"hgvs_c": "c.12200C>T",
"hgvs_p": "p.Pro4067Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011512982.1",
"strand": false,
"transcript": "XM_011514680.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 4074,
"aa_ref": "P",
"aa_start": 4067,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 16109,
"cdna_start": 12302,
"cds_end": null,
"cds_length": 12225,
"cds_start": 12200,
"consequences": [
"missense_variant"
],
"exon_count": 67,
"exon_rank": 67,
"exon_rank_end": null,
"feature": "XM_017010944.3",
"gene_hgnc_id": 9016,
"gene_symbol": "PKHD1",
"hgvs_c": "c.12200C>T",
"hgvs_p": "p.Pro4067Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016866433.1",
"strand": false,
"transcript": "XM_017010944.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 4049,
"aa_ref": "P",
"aa_start": 4042,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 16196,
"cdna_start": 12389,
"cds_end": null,
"cds_length": 12150,
"cds_start": 12125,
"consequences": [
"missense_variant"
],
"exon_count": 66,
"exon_rank": 66,
"exon_rank_end": null,
"feature": "XM_017010945.3",
"gene_hgnc_id": 9016,
"gene_symbol": "PKHD1",
"hgvs_c": "c.12125C>T",
"hgvs_p": "p.Pro4042Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016866434.1",
"strand": false,
"transcript": "XM_017010945.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 4028,
"aa_ref": "P",
"aa_start": 4021,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 16133,
"cdna_start": 12326,
"cds_end": null,
"cds_length": 12087,
"cds_start": 12062,
"consequences": [
"missense_variant"
],
"exon_count": 66,
"exon_rank": 66,
"exon_rank_end": null,
"feature": "XM_011514682.4",
"gene_hgnc_id": 9016,
"gene_symbol": "PKHD1",
"hgvs_c": "c.12062C>T",
"hgvs_p": "p.Pro4021Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011512984.1",
"strand": false,
"transcript": "XM_011514682.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 4009,
"aa_ref": "P",
"aa_start": 4002,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 16076,
"cdna_start": 12269,
"cds_end": null,
"cds_length": 12030,
"cds_start": 12005,
"consequences": [
"missense_variant"
],
"exon_count": 65,
"exon_rank": 65,
"exon_rank_end": null,
"feature": "XM_017010946.3",
"gene_hgnc_id": 9016,
"gene_symbol": "PKHD1",
"hgvs_c": "c.12005C>T",
"hgvs_p": "p.Pro4002Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016866435.1",
"strand": false,
"transcript": "XM_017010946.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 3986,
"aa_ref": "P",
"aa_start": 3979,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 16007,
"cdna_start": 12200,
"cds_end": null,
"cds_length": 11961,
"cds_start": 11936,
"consequences": [
"missense_variant"
],
"exon_count": 65,
"exon_rank": 65,
"exon_rank_end": null,
"feature": "XM_017010947.3",
"gene_hgnc_id": 9016,
"gene_symbol": "PKHD1",
"hgvs_c": "c.11936C>T",
"hgvs_p": "p.Pro3979Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016866436.1",
"strand": false,
"transcript": "XM_017010947.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 3860,
"aa_ref": "P",
"aa_start": 3853,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15629,
"cdna_start": 11822,
"cds_end": null,
"cds_length": 11583,
"cds_start": 11558,
"consequences": [
"missense_variant"
],
"exon_count": 68,
"exon_rank": 68,
"exon_rank_end": null,
"feature": "XM_011514683.4",
"gene_hgnc_id": 9016,
"gene_symbol": "PKHD1",
"hgvs_c": "c.11558C>T",
"hgvs_p": "p.Pro3853Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011512985.1",
"strand": false,
"transcript": "XM_011514683.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 3837,
"aa_ref": "P",
"aa_start": 3830,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15393,
"cdna_start": 11586,
"cds_end": null,
"cds_length": 11514,
"cds_start": 11489,
"consequences": [
"missense_variant"
],
"exon_count": 59,
"exon_rank": 59,
"exon_rank_end": null,
"feature": "XM_011514684.4",
"gene_hgnc_id": 9016,
"gene_symbol": "PKHD1",
"hgvs_c": "c.11489C>T",
"hgvs_p": "p.Pro3830Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011512986.1",
"strand": false,
"transcript": "XM_011514684.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 3837,
"aa_ref": "P",
"aa_start": 3830,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 16067,
"cdna_start": 12260,
"cds_end": null,
"cds_length": 11514,
"cds_start": 11489,
"consequences": [
"missense_variant"
],
"exon_count": 58,
"exon_rank": 58,
"exon_rank_end": null,
"feature": "XM_017010948.3",
"gene_hgnc_id": 9016,
"gene_symbol": "PKHD1",
"hgvs_c": "c.11489C>T",
"hgvs_p": "p.Pro3830Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016866437.1",
"strand": false,
"transcript": "XM_017010948.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 3454,
"aa_ref": "P",
"aa_start": 3447,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15246,
"cdna_start": 11439,
"cds_end": null,
"cds_length": 10365,
"cds_start": 10340,
"consequences": [
"missense_variant"
],
"exon_count": 49,
"exon_rank": 49,
"exon_rank_end": null,
"feature": "XM_017010949.3",
"gene_hgnc_id": 9016,
"gene_symbol": "PKHD1",
"hgvs_c": "c.10340C>T",
"hgvs_p": "p.Pro3447Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016866438.1",
"strand": false,
"transcript": "XM_017010949.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 2099,
"aa_ref": "P",
"aa_start": 2092,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10169,
"cdna_start": 6362,
"cds_end": null,
"cds_length": 6300,
"cds_start": 6275,
"consequences": [
"missense_variant"
],
"exon_count": 32,
"exon_rank": 32,
"exon_rank_end": null,
"feature": "XM_011514690.4",
"gene_hgnc_id": 9016,
"gene_symbol": "PKHD1",
"hgvs_c": "c.6275C>T",
"hgvs_p": "p.Pro2092Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011512992.1",
"strand": false,
"transcript": "XM_011514690.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 2099,
"aa_ref": "P",
"aa_start": 2092,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 16191,
"cdna_start": 12384,
"cds_end": null,
"cds_length": 6300,
"cds_start": 6275,
"consequences": [
"missense_variant"
],
"exon_count": 32,
"exon_rank": 32,
"exon_rank_end": null,
"feature": "XM_011514691.4",
"gene_hgnc_id": 9016,
"gene_symbol": "PKHD1",
"hgvs_c": "c.6275C>T",
"hgvs_p": "p.Pro2092Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011512993.1",
"strand": false,
"transcript": "XM_011514691.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 610,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000454361.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000228689",
"hgvs_c": "n.81-3249G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000454361.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 992,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000589278.6",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000228689",
"hgvs_c": "n.811-3254G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000589278.6",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1295,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000650088.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000228689",
"hgvs_c": "n.222-3249G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000650088.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs758871283",
"effect": "missense_variant",
"frequency_reference_population": 0.00001548776,
"gene_hgnc_id": 9016,
"gene_symbol": "PKHD1",
"gnomad_exomes_ac": 20,
"gnomad_exomes_af": 0.0000136816,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 5,
"gnomad_genomes_af": 0.000032817,
"gnomad_genomes_homalt": 0,
"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": "Autosomal recessive polycystic kidney disease|not provided|Polycystic kidney disease 4",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.758,
"pos": 51619106,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.16,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_138694.4"
}
]
}