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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: 2-55579177-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=55579177&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 55579177,
"ref": "C",
"alt": "T",
"effect": "intron_variant",
"transcript": "ENST00000616407.2",
"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": 17,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PPP4R3B",
"gene_hgnc_id": 29267,
"hgvs_c": "c.1468+502G>A",
"hgvs_p": null,
"transcript": "NM_001122964.3",
"protein_id": "NP_001116436.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 849,
"cds_start": -4,
"cds_end": null,
"cds_length": 2550,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5506,
"mane_select": "ENST00000616407.2",
"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": 17,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PPP4R3B",
"gene_hgnc_id": 29267,
"hgvs_c": "c.1468+502G>A",
"hgvs_p": null,
"transcript": "ENST00000616407.2",
"protein_id": "ENSP00000483228.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 849,
"cds_start": -4,
"cds_end": null,
"cds_length": 2550,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5506,
"mane_select": "NM_001122964.3",
"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": 9,
"intron_rank_end": null,
"gene_symbol": "PPP4R3B",
"gene_hgnc_id": 29267,
"hgvs_c": "c.1468+502G>A",
"hgvs_p": null,
"transcript": "ENST00000616288.4",
"protein_id": "ENSP00000484116.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 817,
"cds_start": -4,
"cds_end": null,
"cds_length": 2454,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4310,
"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": 15,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PPP4R3B",
"gene_hgnc_id": 29267,
"hgvs_c": "c.1468+502G>A",
"hgvs_p": null,
"transcript": "ENST00000611717.4",
"protein_id": "ENSP00000478677.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 764,
"cds_start": -4,
"cds_end": null,
"cds_length": 2295,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5243,
"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": 9,
"intron_rank_end": null,
"gene_symbol": "PPP4R3B",
"gene_hgnc_id": 29267,
"hgvs_c": "c.1468+502G>A",
"hgvs_p": null,
"transcript": "NM_001282850.2",
"protein_id": "NP_001269779.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 817,
"cds_start": -4,
"cds_end": null,
"cds_length": 2454,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5410,
"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": 15,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PPP4R3B",
"gene_hgnc_id": 29267,
"hgvs_c": "c.1468+502G>A",
"hgvs_p": null,
"transcript": "NM_020463.4",
"protein_id": "NP_065196.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 764,
"cds_start": -4,
"cds_end": null,
"cds_length": 2295,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5251,
"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": 17,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PPP4R3B",
"gene_hgnc_id": 29267,
"hgvs_c": "c.1468+502G>A",
"hgvs_p": null,
"transcript": "XM_005264442.4",
"protein_id": "XP_005264499.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 842,
"cds_start": -4,
"cds_end": null,
"cds_length": 2529,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5485,
"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": 9,
"intron_rank_end": null,
"gene_symbol": "PPP4R3B",
"gene_hgnc_id": 29267,
"hgvs_c": "c.1468+502G>A",
"hgvs_p": null,
"transcript": "XM_017004531.3",
"protein_id": "XP_016860020.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 810,
"cds_start": -4,
"cds_end": null,
"cds_length": 2433,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5389,
"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": 9,
"intron_rank_end": null,
"gene_symbol": "PPP4R3B",
"gene_hgnc_id": 29267,
"hgvs_c": "c.1468+502G>A",
"hgvs_p": null,
"transcript": "XM_005264444.4",
"protein_id": "XP_005264501.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 796,
"cds_start": -4,
"cds_end": null,
"cds_length": 2391,
"cdna_start": null,
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"cdna_length": 5347,
"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,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PPP4R3B",
"gene_hgnc_id": 29267,
"hgvs_c": "c.1468+502G>A",
"hgvs_p": null,
"transcript": "XM_005264445.4",
"protein_id": "XP_005264502.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 789,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 15,
"intron_rank": 9,
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"gene_symbol": "PPP4R3B",
"gene_hgnc_id": 29267,
"hgvs_c": "c.1468+502G>A",
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"transcript": "XM_005264446.4",
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},
{
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"strand": false,
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],
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},
{
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],
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"gene_symbol": "PPP4R3B",
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},
{
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"strand": false,
"consequences": [
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],
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"gene_symbol": "PPP4R3B",
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},
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],
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"gene_symbol": "PPP4R3B",
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"hgvs_c": "c.844+502G>A",
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},
{
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],
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"hgvs_c": "c.844+502G>A",
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],
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},
{
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],
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"intron_rank": 8,
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"gene_symbol": "PPP4R3B",
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},
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],
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],
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},
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],
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},
{
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"consequences": [
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],
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"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PPP4R3B",
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"hgvs_c": "c.553+502G>A",
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"transcript": "XM_047445155.1",
"protein_id": "XP_047301111.1",
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"feature": null
}
],
"gene_symbol": "PPP4R3B",
"gene_hgnc_id": 29267,
"dbsnp": "rs10496050",
"frequency_reference_population": 0.447375,
"hom_count_reference_population": 16060,
"allele_count_reference_population": 67950,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.447375,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 67950,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 16060,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.949999988079071,
"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": -0.95,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.283,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000616407.2",
"gene_symbol": "PPP4R3B",
"hgnc_id": 29267,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1468+502G>A",
"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
}