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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: 6-51791359-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=51791359&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 51791359,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000371117.8",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 53,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8317G>A",
"hgvs_p": "p.Val2773Met",
"transcript": "NM_138694.4",
"protein_id": "NP_619639.3",
"transcript_support_level": null,
"aa_start": 2773,
"aa_end": null,
"aa_length": 4074,
"cds_start": 8317,
"cds_end": null,
"cds_length": 12225,
"cdna_start": 8581,
"cdna_end": null,
"cdna_length": 16271,
"mane_select": "ENST00000371117.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 53,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8317G>A",
"hgvs_p": "p.Val2773Met",
"transcript": "ENST00000371117.8",
"protein_id": "ENSP00000360158.3",
"transcript_support_level": 1,
"aa_start": 2773,
"aa_end": null,
"aa_length": 4074,
"cds_start": 8317,
"cds_end": null,
"cds_length": 12225,
"cdna_start": 8581,
"cdna_end": null,
"cdna_length": 16271,
"mane_select": "NM_138694.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 53,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8317G>A",
"hgvs_p": "p.Val2773Met",
"transcript": "NM_170724.3",
"protein_id": "NP_733842.2",
"transcript_support_level": null,
"aa_start": 2773,
"aa_end": null,
"aa_length": 3396,
"cds_start": 8317,
"cds_end": null,
"cds_length": 10191,
"cdna_start": 8581,
"cdna_end": null,
"cdna_length": 11592,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 53,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8317G>A",
"hgvs_p": "p.Val2773Met",
"transcript": "ENST00000340994.4",
"protein_id": "ENSP00000341097.4",
"transcript_support_level": 5,
"aa_start": 2773,
"aa_end": null,
"aa_length": 3396,
"cds_start": 8317,
"cds_end": null,
"cds_length": 10191,
"cdna_start": 8578,
"cdna_end": null,
"cdna_length": 11589,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 53,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8317G>A",
"hgvs_p": "p.Val2773Met",
"transcript": "XM_011514680.4",
"protein_id": "XP_011512982.1",
"transcript_support_level": null,
"aa_start": 2773,
"aa_end": null,
"aa_length": 4074,
"cds_start": 8317,
"cds_end": null,
"cds_length": 12225,
"cdna_start": 8940,
"cdna_end": null,
"cdna_length": 16630,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 53,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8317G>A",
"hgvs_p": "p.Val2773Met",
"transcript": "XM_017010944.3",
"protein_id": "XP_016866433.1",
"transcript_support_level": null,
"aa_start": 2773,
"aa_end": null,
"aa_length": 4074,
"cds_start": 8317,
"cds_end": null,
"cds_length": 12225,
"cdna_start": 8419,
"cdna_end": null,
"cdna_length": 16109,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 52,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8242G>A",
"hgvs_p": "p.Val2748Met",
"transcript": "XM_017010945.3",
"protein_id": "XP_016866434.1",
"transcript_support_level": null,
"aa_start": 2748,
"aa_end": null,
"aa_length": 4049,
"cds_start": 8242,
"cds_end": null,
"cds_length": 12150,
"cdna_start": 8506,
"cdna_end": null,
"cdna_length": 16196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 51,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8122G>A",
"hgvs_p": "p.Val2708Met",
"transcript": "XM_017010946.3",
"protein_id": "XP_016866435.1",
"transcript_support_level": null,
"aa_start": 2708,
"aa_end": null,
"aa_length": 4009,
"cds_start": 8122,
"cds_end": null,
"cds_length": 12030,
"cdna_start": 8386,
"cdna_end": null,
"cdna_length": 16076,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 51,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8053G>A",
"hgvs_p": "p.Val2685Met",
"transcript": "XM_017010947.3",
"protein_id": "XP_016866436.1",
"transcript_support_level": null,
"aa_start": 2685,
"aa_end": null,
"aa_length": 3986,
"cds_start": 8053,
"cds_end": null,
"cds_length": 11961,
"cdna_start": 8317,
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"cdna_length": 16007,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 54,
"exon_rank_end": null,
"exon_count": 68,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.7675G>A",
"hgvs_p": "p.Val2559Met",
"transcript": "XM_011514683.4",
"protein_id": "XP_011512985.1",
"transcript_support_level": null,
"aa_start": 2559,
"aa_end": null,
"aa_length": 3860,
"cds_start": 7675,
"cds_end": null,
"cds_length": 11583,
"cdna_start": 7939,
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"cdna_length": 15629,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
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"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.7606G>A",
"hgvs_p": "p.Val2536Met",
"transcript": "XM_011514684.4",
"protein_id": "XP_011512986.1",
"transcript_support_level": null,
"aa_start": 2536,
"aa_end": null,
"aa_length": 3837,
"cds_start": 7606,
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"cdna_start": 7703,
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},
{
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"consequences": [
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],
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"exon_count": 58,
"intron_rank": null,
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"gene_symbol": "PKHD1",
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"hgvs_p": "p.Val2536Met",
"transcript": "XM_017010948.3",
"protein_id": "XP_016866437.1",
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"aa_start": 2536,
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"cds_start": 7606,
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"cdna_start": 8377,
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"feature": null
},
{
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"strand": false,
"consequences": [
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],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
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"gene_symbol": "PKHD1",
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"hgvs_p": "p.Val2153Met",
"transcript": "XM_017010949.3",
"protein_id": "XP_016866438.1",
"transcript_support_level": null,
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},
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],
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"intron_rank": null,
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"gene_symbol": "PKHD1",
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},
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"strand": false,
"consequences": [
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],
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"intron_rank": null,
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"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8317G>A",
"hgvs_p": "p.Val2773Met",
"transcript": "XM_017010950.2",
"protein_id": "XP_016866439.1",
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},
{
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],
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"intron_rank": null,
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"gene_symbol": "PKHD1",
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"transcript": "XM_011514686.3",
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},
{
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"consequences": [
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"exon_rank": 53,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
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"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8317G>A",
"hgvs_p": "p.Val2773Met",
"transcript": "XM_011514687.2",
"protein_id": "XP_011512989.1",
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"feature": null
},
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"protein_coding": true,
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"consequences": [
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"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
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"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8317G>A",
"hgvs_p": "p.Val2773Met",
"transcript": "XM_011514688.3",
"protein_id": "XP_011512990.1",
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},
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"gene_symbol": "PKHD1",
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"hgvs_c": "c.8317G>A",
"hgvs_p": "p.Val2773Met",
"transcript": "XM_017010951.2",
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"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
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"hgvs_p": "p.Val2773Met",
"transcript": "XM_047418895.1",
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},
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],
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"gene_symbol": "PKHD1",
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"hgvs_p": "p.Val798Met",
"transcript": "XM_011514690.4",
"protein_id": "XP_011512992.1",
"transcript_support_level": null,
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"feature": null
},
{
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"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.2392G>A",
"hgvs_p": "p.Val798Met",
"transcript": "XM_011514691.4",
"protein_id": "XP_011512993.1",
"transcript_support_level": null,
"aa_start": 798,
"aa_end": null,
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"cds_start": 2392,
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"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 53,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
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"gene_symbol": "PKHD1",
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"hgvs_c": "n.8581G>A",
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"transcript": "XR_001743469.2",
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"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cds_length": null,
"cdna_start": null,
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"cdna_length": 11764,
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"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": 66,
"intron_rank": 52,
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"gene_symbol": "PKHD1",
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"hgvs_c": "c.8303-15438G>A",
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"transcript": "XM_011514682.4",
"protein_id": "XP_011512984.1",
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"aa_start": null,
"aa_end": null,
"aa_length": 4028,
"cds_start": -4,
"cds_end": null,
"cds_length": 12087,
"cdna_start": null,
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"cdna_length": 16133,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"dbsnp": "rs747322128",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.915208101272583,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.601,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3719,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.12,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.239,
"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": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Moderate",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000371117.8",
"gene_symbol": "PKHD1",
"hgnc_id": 9016,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.8317G>A",
"hgvs_p": "p.Val2773Met"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}