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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: 18-57697598-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=57697598&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "18",
"pos": 57697598,
"ref": "G",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000648908.2",
"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": 28,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "ATP8B1",
"gene_hgnc_id": 3706,
"hgvs_c": "c.698+20C>T",
"hgvs_p": null,
"transcript": "NM_001374385.1",
"protein_id": "NP_001361314.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1251,
"cds_start": -4,
"cds_end": null,
"cds_length": 3756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6161,
"mane_select": "ENST00000648908.2",
"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": 28,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "ATP8B1",
"gene_hgnc_id": 3706,
"hgvs_c": "c.698+20C>T",
"hgvs_p": null,
"transcript": "ENST00000648908.2",
"protein_id": "ENSP00000497896.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1251,
"cds_start": -4,
"cds_end": null,
"cds_length": 3756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6161,
"mane_select": "NM_001374385.1",
"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": 28,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "ATP8B1",
"gene_hgnc_id": 3706,
"hgvs_c": "c.698+20C>T",
"hgvs_p": null,
"transcript": "NM_005603.6",
"protein_id": "NP_005594.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1251,
"cds_start": -4,
"cds_end": null,
"cds_length": 3756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6158,
"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": 27,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "ATP8B1",
"gene_hgnc_id": 3706,
"hgvs_c": "c.548+20C>T",
"hgvs_p": null,
"transcript": "NM_001374386.1",
"protein_id": "NP_001361315.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1201,
"cds_start": -4,
"cds_end": null,
"cds_length": 3606,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6063,
"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": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ATP8B1-AS1",
"gene_hgnc_id": 56042,
"hgvs_c": "n.571-33816G>A",
"hgvs_p": null,
"transcript": "ENST00000588925.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 1976,
"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": 29,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "ATP8B1",
"gene_hgnc_id": 3706,
"hgvs_c": "n.698+20C>T",
"hgvs_p": null,
"transcript": "ENST00000642462.1",
"protein_id": "ENSP00000494712.1",
"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": 5956,
"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": 29,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "ATP8B1",
"gene_hgnc_id": 3706,
"hgvs_c": "n.698+20C>T",
"hgvs_p": null,
"transcript": "ENST00000648039.1",
"protein_id": "ENSP00000497863.1",
"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,
"cdna_end": null,
"cdna_length": 5919,
"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": 16,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "ATP8B1",
"gene_hgnc_id": 3706,
"hgvs_c": "n.530+20C>T",
"hgvs_p": null,
"transcript": "ENST00000648467.1",
"protein_id": "ENSP00000496933.1",
"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": 1857,
"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": 1,
"intron_rank_end": null,
"gene_symbol": "ATP8B1-AS1",
"gene_hgnc_id": 56042,
"hgvs_c": "n.79+1562G>A",
"hgvs_p": null,
"transcript": "ENST00000649476.1",
"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": 1363,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ATP8B1-AS1",
"gene_hgnc_id": 56042,
"hgvs_c": "n.1784+1562G>A",
"hgvs_p": null,
"transcript": "ENST00000660188.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
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"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 2125,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 3,
"intron_rank": 2,
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"gene_symbol": "ATP8B1-AS1",
"gene_hgnc_id": 56042,
"hgvs_c": "n.309-40935G>A",
"hgvs_p": null,
"transcript": "ENST00000794640.1",
"protein_id": null,
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},
{
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"protein_coding": false,
"strand": true,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 3,
"intron_rank": 2,
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"gene_symbol": "ATP8B1-AS1",
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"hgvs_c": "n.311-37553G>A",
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"transcript": "ENST00000794776.1",
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},
{
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"strand": true,
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],
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"gene_symbol": "ATP8B1-AS1",
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"hgvs_c": "n.462+1562G>A",
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"transcript": "ENST00000794777.1",
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},
{
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"strand": true,
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],
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"gene_symbol": "ATP8B1-AS1",
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"hgvs_c": "n.683-33816G>A",
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"transcript": "ENST00000794778.1",
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},
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],
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"intron_rank": 8,
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"gene_symbol": "ATP8B1",
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"hgvs_c": "c.698+20C>T",
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"transcript": "XM_047437541.1",
"protein_id": "XP_047293497.1",
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},
{
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"consequences": [
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],
"exon_rank": null,
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"intron_rank": 8,
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"gene_symbol": "ATP8B1",
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"hgvs_c": "c.698+20C>T",
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"transcript": "XM_047437542.1",
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},
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],
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"gene_symbol": "ATP8B1",
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"hgvs_c": "c.698+20C>T",
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"transcript": "XM_047437543.1",
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},
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],
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"intron_rank": 8,
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"gene_symbol": "ATP8B1",
"gene_hgnc_id": 3706,
"hgvs_c": "c.698+20C>T",
"hgvs_p": null,
"transcript": "XM_047437544.1",
"protein_id": "XP_047293500.1",
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},
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"consequences": [
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],
"exon_rank": null,
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"intron_rank": 8,
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"gene_symbol": "ATP8B1",
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"hgvs_c": "c.698+20C>T",
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"transcript": "XM_047437545.1",
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},
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],
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"gene_symbol": "ATP8B1",
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},
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"consequences": [
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],
"exon_rank": null,
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"exon_count": 27,
"intron_rank": 7,
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"gene_symbol": "ATP8B1",
"gene_hgnc_id": 3706,
"hgvs_c": "c.584+20C>T",
"hgvs_p": null,
"transcript": "XM_047437547.1",
"protein_id": "XP_047293503.1",
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},
{
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"consequences": [
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],
"exon_rank": null,
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"exon_count": 27,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "ATP8B1",
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"hgvs_c": "c.584+20C>T",
"hgvs_p": null,
"transcript": "XM_047437548.1",
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},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP8B1",
"gene_hgnc_id": 3706,
"hgvs_c": "n.*72C>T",
"hgvs_p": null,
"transcript": "ENST00000589147.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 540,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATP8B1",
"gene_hgnc_id": 3706,
"dbsnp": "rs319439",
"frequency_reference_population": 0.47240052,
"hom_count_reference_population": 184694,
"allele_count_reference_population": 760066,
"gnomad_exomes_af": 0.476791,
"gnomad_genomes_af": 0.430283,
"gnomad_exomes_ac": 694706,
"gnomad_genomes_ac": 65360,
"gnomad_exomes_homalt": 169620,
"gnomad_genomes_homalt": 15074,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8100000023841858,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.81,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.221,
"phylop100way_prediction": "Benign",
"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": -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": "ENST00000648908.2",
"gene_symbol": "ATP8B1",
"hgnc_id": 3706,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.698+20C>T",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000588925.5",
"gene_symbol": "ATP8B1-AS1",
"hgnc_id": 56042,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.571-33816G>A",
"hgvs_p": null
}
],
"clinvar_disease": " 1, intrahepatic, of pregnancy,Cholestasis,Progressive familial intrahepatic cholestasis type 1,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:6",
"phenotype_combined": "not specified|Cholestasis, intrahepatic, of pregnancy, 1|Progressive familial intrahepatic cholestasis type 1|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}