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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: X-139614790-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=139614790&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 139614790,
"ref": "C",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000519895.6",
"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": 29,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "MCF2",
"gene_hgnc_id": 6940,
"hgvs_c": "c.1543+91G>T",
"hgvs_p": null,
"transcript": "NM_001171876.2",
"protein_id": "NP_001165347.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1001,
"cds_start": -4,
"cds_end": null,
"cds_length": 3006,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3813,
"mane_select": "ENST00000519895.6",
"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": 29,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "MCF2",
"gene_hgnc_id": 6940,
"hgvs_c": "c.1543+91G>T",
"hgvs_p": null,
"transcript": "ENST00000519895.6",
"protein_id": "ENSP00000430276.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 1001,
"cds_start": -4,
"cds_end": null,
"cds_length": 3006,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3813,
"mane_select": "NM_001171876.2",
"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": 26,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "MCF2",
"gene_hgnc_id": 6940,
"hgvs_c": "c.1363+91G>T",
"hgvs_p": null,
"transcript": "ENST00000338585.6",
"protein_id": "ENSP00000342204.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 941,
"cds_start": -4,
"cds_end": null,
"cds_length": 2826,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2826,
"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": 25,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "MCF2",
"gene_hgnc_id": 6940,
"hgvs_c": "c.1363+91G>T",
"hgvs_p": null,
"transcript": "ENST00000370576.9",
"protein_id": "ENSP00000359608.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 925,
"cds_start": -4,
"cds_end": null,
"cds_length": 2778,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3864,
"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": 23,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "MCF2",
"gene_hgnc_id": 6940,
"hgvs_c": "c.1363+91G>T",
"hgvs_p": null,
"transcript": "ENST00000370573.8",
"protein_id": "ENSP00000359605.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 860,
"cds_start": -4,
"cds_end": null,
"cds_length": 2583,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2583,
"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": 16,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MCF2",
"gene_hgnc_id": 6940,
"hgvs_c": "c.172+91G>T",
"hgvs_p": null,
"transcript": "ENST00000446225.5",
"protein_id": "ENSP00000405848.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 528,
"cds_start": -4,
"cds_end": null,
"cds_length": 1587,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1916,
"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": 28,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "MCF2",
"gene_hgnc_id": 6940,
"hgvs_c": "c.1672+91G>T",
"hgvs_p": null,
"transcript": "ENST00000520602.6",
"protein_id": "ENSP00000427745.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1028,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 3945,
"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": 28,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "MCF2",
"gene_hgnc_id": 6940,
"hgvs_c": "c.1543+91G>T",
"hgvs_p": null,
"transcript": "NM_001099855.2",
"protein_id": "NP_001093325.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 985,
"cds_start": -4,
"cds_end": null,
"cds_length": 2958,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3765,
"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": 28,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "MCF2",
"gene_hgnc_id": 6940,
"hgvs_c": "c.1543+91G>T",
"hgvs_p": null,
"transcript": "ENST00000414978.5",
"protein_id": "ENSP00000397055.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 985,
"cds_start": -4,
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"cds_length": 2958,
"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 26,
"intron_rank": 10,
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"gene_symbol": "MCF2",
"gene_hgnc_id": 6940,
"hgvs_c": "c.1363+91G>T",
"hgvs_p": null,
"transcript": "NM_001171879.2",
"protein_id": "NP_001165350.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": 941,
"cds_start": -4,
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 25,
"intron_rank": 10,
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"gene_symbol": "MCF2",
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"hgvs_c": "c.1363+91G>T",
"hgvs_p": null,
"transcript": "NM_005369.6",
"protein_id": "NP_005360.3",
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},
{
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],
"exon_rank": null,
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"gene_symbol": "MCF2",
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"transcript": "NM_001171878.2",
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},
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],
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"gene_symbol": "MCF2",
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"hgvs_c": "c.1246+91G>T",
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},
{
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],
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"gene_symbol": "MCF2",
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],
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},
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],
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"gene_symbol": "MCF2",
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"hgvs_c": "c.1672+91G>T",
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},
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],
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"gene_symbol": "MCF2",
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"transcript": "XM_011531339.3",
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],
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"gene_symbol": "MCF2",
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"hgvs_c": "c.1363+91G>T",
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"transcript": "XM_017029532.3",
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},
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],
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"intron_rank": 10,
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"gene_symbol": "MCF2",
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"transcript": "XM_047442113.1",
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"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": 19,
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"gene_symbol": "MCF2",
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"hgvs_c": "c.385+91G>T",
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"transcript": "XM_047442114.1",
"protein_id": "XP_047298070.1",
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"aa_start": null,
"aa_end": null,
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"cds_start": -4,
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"cds_length": 1800,
"cdna_start": null,
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"cdna_length": 2704,
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"mane_plus": null,
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"feature": null
}
],
"gene_symbol": "MCF2",
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"dbsnp": "rs2076500",
"frequency_reference_population": 0.0000023754267,
"hom_count_reference_population": 1,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136791,
"gnomad_genomes_af": 0.00000901608,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -1,
"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": -1,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.097,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000519895.6",
"gene_symbol": "MCF2",
"hgnc_id": 6940,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1543+91G>T",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}