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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: 7-87402169-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=87402169&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 87402169,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000443.4",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB4",
"gene_hgnc_id": 45,
"hgvs_c": "c.3767A>T",
"hgvs_p": "p.His1256Leu",
"transcript": "NM_000443.4",
"protein_id": "NP_000434.1",
"transcript_support_level": null,
"aa_start": 1256,
"aa_end": null,
"aa_length": 1279,
"cds_start": 3767,
"cds_end": null,
"cds_length": 3840,
"cdna_start": 3820,
"cdna_end": null,
"cdna_length": 4293,
"mane_select": "ENST00000649586.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB4",
"gene_hgnc_id": 45,
"hgvs_c": "c.3767A>T",
"hgvs_p": "p.His1256Leu",
"transcript": "ENST00000649586.2",
"protein_id": "ENSP00000496956.2",
"transcript_support_level": null,
"aa_start": 1256,
"aa_end": null,
"aa_length": 1279,
"cds_start": 3767,
"cds_end": null,
"cds_length": 3840,
"cdna_start": 3820,
"cdna_end": null,
"cdna_length": 4293,
"mane_select": "NM_000443.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB4",
"gene_hgnc_id": 45,
"hgvs_c": "c.3788A>T",
"hgvs_p": "p.His1263Leu",
"transcript": "ENST00000265723.8",
"protein_id": "ENSP00000265723.4",
"transcript_support_level": 1,
"aa_start": 1263,
"aa_end": null,
"aa_length": 1286,
"cds_start": 3788,
"cds_end": null,
"cds_length": 3861,
"cdna_start": 3900,
"cdna_end": null,
"cdna_length": 4020,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB4",
"gene_hgnc_id": 45,
"hgvs_c": "c.3767A>T",
"hgvs_p": "p.His1256Leu",
"transcript": "ENST00000359206.8",
"protein_id": "ENSP00000352135.3",
"transcript_support_level": 1,
"aa_start": 1256,
"aa_end": null,
"aa_length": 1279,
"cds_start": 3767,
"cds_end": null,
"cds_length": 3840,
"cdna_start": 3851,
"cdna_end": null,
"cdna_length": 3961,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB4",
"gene_hgnc_id": 45,
"hgvs_c": "c.3788A>T",
"hgvs_p": "p.His1263Leu",
"transcript": "NM_018849.3",
"protein_id": "NP_061337.1",
"transcript_support_level": null,
"aa_start": 1263,
"aa_end": null,
"aa_length": 1286,
"cds_start": 3788,
"cds_end": null,
"cds_length": 3861,
"cdna_start": 3841,
"cdna_end": null,
"cdna_length": 4314,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB4",
"gene_hgnc_id": 45,
"hgvs_c": "c.3626A>T",
"hgvs_p": "p.His1209Leu",
"transcript": "NM_018850.3",
"protein_id": "NP_061338.1",
"transcript_support_level": null,
"aa_start": 1209,
"aa_end": null,
"aa_length": 1232,
"cds_start": 3626,
"cds_end": null,
"cds_length": 3699,
"cdna_start": 3679,
"cdna_end": null,
"cdna_length": 4152,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB4",
"gene_hgnc_id": 45,
"hgvs_c": "c.3626A>T",
"hgvs_p": "p.His1209Leu",
"transcript": "ENST00000453593.5",
"protein_id": "ENSP00000392983.1",
"transcript_support_level": 5,
"aa_start": 1209,
"aa_end": null,
"aa_length": 1232,
"cds_start": 3626,
"cds_end": null,
"cds_length": 3699,
"cdna_start": 3626,
"cdna_end": null,
"cdna_length": 3699,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB4",
"gene_hgnc_id": 45,
"hgvs_c": "c.200A>T",
"hgvs_p": "p.His67Leu",
"transcript": "ENST00000440025.1",
"protein_id": "ENSP00000395716.1",
"transcript_support_level": 3,
"aa_start": 67,
"aa_end": null,
"aa_length": 98,
"cds_start": 200,
"cds_end": null,
"cds_length": 297,
"cdna_start": 201,
"cdna_end": null,
"cdna_length": 523,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB4",
"gene_hgnc_id": 45,
"hgvs_c": "c.3788A>T",
"hgvs_p": "p.His1263Leu",
"transcript": "XM_011516308.4",
"protein_id": "XP_011514610.4",
"transcript_support_level": null,
"aa_start": 1263,
"aa_end": null,
"aa_length": 1294,
"cds_start": 3788,
"cds_end": null,
"cds_length": 3885,
"cdna_start": 4051,
"cdna_end": null,
"cdna_length": 4374,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB4",
"gene_hgnc_id": 45,
"hgvs_c": "c.3767A>T",
"hgvs_p": "p.His1256Leu",
"transcript": "XM_011516309.4",
"protein_id": "XP_011514611.4",
"transcript_support_level": null,
"aa_start": 1256,
"aa_end": null,
"aa_length": 1287,
"cds_start": 3767,
"cds_end": null,
"cds_length": 3864,
"cdna_start": 4030,
"cdna_end": null,
"cdna_length": 4353,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB4",
"gene_hgnc_id": 45,
"hgvs_c": "c.3647A>T",
"hgvs_p": "p.His1216Leu",
"transcript": "XM_047420475.1",
"protein_id": "XP_047276431.1",
"transcript_support_level": null,
"aa_start": 1216,
"aa_end": null,
"aa_length": 1247,
"cds_start": 3647,
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"cds_length": 3744,
"cdna_start": 3700,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB4",
"gene_hgnc_id": 45,
"hgvs_c": "c.3521A>T",
"hgvs_p": "p.His1174Leu",
"transcript": "XM_047420476.1",
"protein_id": "XP_047276432.1",
"transcript_support_level": null,
"aa_start": 1174,
"aa_end": null,
"aa_length": 1197,
"cds_start": 3521,
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"cds_length": 3594,
"cdna_start": 3574,
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"cdna_length": 4047,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB4",
"gene_hgnc_id": 45,
"hgvs_c": "n.379A>T",
"hgvs_p": null,
"transcript": "ENST00000467983.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"mane_select": null,
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},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
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"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
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"gene_symbol": "ABCB4",
"gene_hgnc_id": 45,
"hgvs_c": "n.4051A>T",
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"transcript": "XR_007060045.1",
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},
{
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"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 27,
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"exon_count": 30,
"intron_rank": null,
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"gene_symbol": "ABCB4",
"gene_hgnc_id": 45,
"hgvs_c": "n.3946A>T",
"hgvs_p": null,
"transcript": "XR_007060046.1",
"protein_id": null,
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"aa_start": null,
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"biotype": null,
"feature": null
},
{
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"protein_coding": false,
"strand": false,
"consequences": [
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],
"exon_rank": 27,
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"exon_count": 30,
"intron_rank": null,
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"gene_symbol": "ABCB4",
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"hgvs_c": "n.3925A>T",
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},
{
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"protein_coding": false,
"strand": false,
"consequences": [
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],
"exon_rank": 28,
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"exon_count": 31,
"intron_rank": null,
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"gene_symbol": "ABCB4",
"gene_hgnc_id": 45,
"hgvs_c": "n.3922A>T",
"hgvs_p": null,
"transcript": "XR_007060048.1",
"protein_id": null,
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},
{
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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": 30,
"intron_rank": null,
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"gene_symbol": "ABCB4",
"gene_hgnc_id": 45,
"hgvs_c": "n.3910A>T",
"hgvs_p": null,
"transcript": "XR_007060049.1",
"protein_id": null,
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},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
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],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
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"gene_symbol": "ABCB4",
"gene_hgnc_id": 45,
"hgvs_c": "n.3889A>T",
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},
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],
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"intron_rank": null,
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"gene_symbol": "ABCB4",
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"hgvs_c": "n.3841A>T",
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},
{
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"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
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"intron_rank": null,
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"gene_symbol": "ABCB4",
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},
{
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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": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB4",
"gene_hgnc_id": 45,
"hgvs_c": "n.3679A>T",
"hgvs_p": null,
"transcript": "XR_007060053.1",
"protein_id": null,
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"aa_start": null,
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"feature": null
},
{
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"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 27,
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"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCB4",
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"hgvs_c": "n.3679A>T",
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"transcript": "XR_007060054.1",
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},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 23,
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"exon_count": 26,
"intron_rank": null,
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"gene_symbol": "ABCB4",
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"transcript": "XR_007060055.1",
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"aa_start": null,
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"cds_start": -4,
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}
],
"gene_symbol": "ABCB4",
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"dbsnp": "rs751933656",
"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": 0.9295693635940552,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.805,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9029,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.31,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.014,
"phylop100way_prediction": "Pathogenic",
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM1",
"PM2",
"PP2",
"PP3_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_000443.4",
"gene_symbol": "ABCB4",
"hgnc_id": 45,
"effects": [
"missense_variant"
],
"inheritance_mode": "SD,AR,AD",
"hgvs_c": "c.3767A>T",
"hgvs_p": "p.His1256Leu"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}