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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: 6-52043020-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=52043020&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 52043020,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000371117.8",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.2936C>T",
"hgvs_p": "p.Thr979Ile",
"transcript": "NM_138694.4",
"protein_id": "NP_619639.3",
"transcript_support_level": null,
"aa_start": 979,
"aa_end": null,
"aa_length": 4074,
"cds_start": 2936,
"cds_end": null,
"cds_length": 12225,
"cdna_start": 3200,
"cdna_end": null,
"cdna_length": 16271,
"mane_select": "ENST00000371117.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.2936C>T",
"hgvs_p": "p.Thr979Ile",
"transcript": "ENST00000371117.8",
"protein_id": "ENSP00000360158.3",
"transcript_support_level": 1,
"aa_start": 979,
"aa_end": null,
"aa_length": 4074,
"cds_start": 2936,
"cds_end": null,
"cds_length": 12225,
"cdna_start": 3200,
"cdna_end": null,
"cdna_length": 16271,
"mane_select": "NM_138694.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.2936C>T",
"hgvs_p": "p.Thr979Ile",
"transcript": "NM_170724.3",
"protein_id": "NP_733842.2",
"transcript_support_level": null,
"aa_start": 979,
"aa_end": null,
"aa_length": 3396,
"cds_start": 2936,
"cds_end": null,
"cds_length": 10191,
"cdna_start": 3200,
"cdna_end": null,
"cdna_length": 11592,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.2936C>T",
"hgvs_p": "p.Thr979Ile",
"transcript": "ENST00000340994.4",
"protein_id": "ENSP00000341097.4",
"transcript_support_level": 5,
"aa_start": 979,
"aa_end": null,
"aa_length": 3396,
"cds_start": 2936,
"cds_end": null,
"cds_length": 10191,
"cdna_start": 3197,
"cdna_end": null,
"cdna_length": 11589,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.2936C>T",
"hgvs_p": "p.Thr979Ile",
"transcript": "XM_011514680.4",
"protein_id": "XP_011512982.1",
"transcript_support_level": null,
"aa_start": 979,
"aa_end": null,
"aa_length": 4074,
"cds_start": 2936,
"cds_end": null,
"cds_length": 12225,
"cdna_start": 3559,
"cdna_end": null,
"cdna_length": 16630,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.2936C>T",
"hgvs_p": "p.Thr979Ile",
"transcript": "XM_017010944.3",
"protein_id": "XP_016866433.1",
"transcript_support_level": null,
"aa_start": 979,
"aa_end": null,
"aa_length": 4074,
"cds_start": 2936,
"cds_end": null,
"cds_length": 12225,
"cdna_start": 3038,
"cdna_end": null,
"cdna_length": 16109,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.2861C>T",
"hgvs_p": "p.Thr954Ile",
"transcript": "XM_017010945.3",
"protein_id": "XP_016866434.1",
"transcript_support_level": null,
"aa_start": 954,
"aa_end": null,
"aa_length": 4049,
"cds_start": 2861,
"cds_end": null,
"cds_length": 12150,
"cdna_start": 3125,
"cdna_end": null,
"cdna_length": 16196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.2936C>T",
"hgvs_p": "p.Thr979Ile",
"transcript": "XM_011514682.4",
"protein_id": "XP_011512984.1",
"transcript_support_level": null,
"aa_start": 979,
"aa_end": null,
"aa_length": 4028,
"cds_start": 2936,
"cds_end": null,
"cds_length": 12087,
"cdna_start": 3200,
"cdna_end": null,
"cdna_length": 16133,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.2936C>T",
"hgvs_p": "p.Thr979Ile",
"transcript": "XM_017010946.3",
"protein_id": "XP_016866435.1",
"transcript_support_level": null,
"aa_start": 979,
"aa_end": null,
"aa_length": 4009,
"cds_start": 2936,
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"cdna_start": 3200,
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"cdna_length": 16076,
"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": 27,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.2936C>T",
"hgvs_p": "p.Thr979Ile",
"transcript": "XM_017010947.3",
"protein_id": "XP_016866436.1",
"transcript_support_level": null,
"aa_start": 979,
"aa_end": null,
"aa_length": 3986,
"cds_start": 2936,
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"cdna_start": 3200,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
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"exon_count": 68,
"intron_rank": null,
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"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.2936C>T",
"hgvs_p": "p.Thr979Ile",
"transcript": "XM_011514683.4",
"protein_id": "XP_011512985.1",
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"aa_start": 979,
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"cds_start": 2936,
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},
{
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"consequences": [
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],
"exon_rank": 19,
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"exon_count": 59,
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"gene_symbol": "PKHD1",
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"transcript": "XM_011514684.4",
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},
{
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"strand": false,
"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.Thr742Ile",
"transcript": "XM_017010948.3",
"protein_id": "XP_016866437.1",
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},
{
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],
"exon_rank": 9,
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"gene_symbol": "PKHD1",
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},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 27,
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"intron_rank": null,
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"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.2936C>T",
"hgvs_p": "p.Thr979Ile",
"transcript": "XM_011514685.2",
"protein_id": "XP_011512987.1",
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},
{
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"strand": false,
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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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"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
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"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.2936C>T",
"hgvs_p": "p.Thr979Ile",
"transcript": "XM_011514686.3",
"protein_id": "XP_011512988.1",
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},
{
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"protein_coding": true,
"strand": false,
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],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
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"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.2936C>T",
"hgvs_p": "p.Thr979Ile",
"transcript": "XM_011514687.2",
"protein_id": "XP_011512989.1",
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},
{
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],
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"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
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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",
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"transcript": "XM_017010951.2",
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},
{
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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.2936C>T",
"hgvs_p": "p.Thr979Ile",
"transcript": "XM_047418895.1",
"protein_id": "XP_047274851.1",
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"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.2936C>T",
"hgvs_p": "p.Thr979Ile",
"transcript": "XM_017010952.2",
"protein_id": "XP_016866441.1",
"transcript_support_level": null,
"aa_start": 979,
"aa_end": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "n.3200C>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
}
],
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"dbsnp": "rs747895516",
"frequency_reference_population": 0.000055145236,
"hom_count_reference_population": 1,
"allele_count_reference_population": 89,
"gnomad_exomes_af": 0.0000595179,
"gnomad_genomes_af": 0.0000131427,
"gnomad_exomes_ac": 87,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9799351692199707,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.651,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.5063,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.27,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.798,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PM1",
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000371117.8",
"gene_symbol": "PKHD1",
"hgnc_id": 9016,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2936C>T",
"hgvs_p": "p.Thr979Ile"
}
],
"clinvar_disease": "Autosomal recessive polycystic kidney disease,Polycystic kidney disease 4",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3 LP:1",
"phenotype_combined": "Autosomal recessive polycystic kidney disease|Polycystic kidney disease 4",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}