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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: 9-120389372-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=120389372&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 120389372,
"ref": "G",
"alt": "A",
"effect": "intron_variant",
"transcript": "NM_018249.6",
"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": 38,
"intron_rank": 37,
"intron_rank_end": null,
"gene_symbol": "CDK5RAP2",
"gene_hgnc_id": 18672,
"hgvs_c": "c.5626-80C>T",
"hgvs_p": null,
"transcript": "NM_018249.6",
"protein_id": "NP_060719.4",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1893,
"cds_start": -4,
"cds_end": null,
"cds_length": 5682,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6232,
"mane_select": "ENST00000349780.9",
"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": 38,
"intron_rank": 37,
"intron_rank_end": null,
"gene_symbol": "CDK5RAP2",
"gene_hgnc_id": 18672,
"hgvs_c": "c.5626-80C>T",
"hgvs_p": null,
"transcript": "ENST00000349780.9",
"protein_id": "ENSP00000343818.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1893,
"cds_start": -4,
"cds_end": null,
"cds_length": 5682,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6232,
"mane_select": "NM_018249.6",
"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": 37,
"intron_rank": 36,
"intron_rank_end": null,
"gene_symbol": "CDK5RAP2",
"gene_hgnc_id": 18672,
"hgvs_c": "c.5389-80C>T",
"hgvs_p": null,
"transcript": "ENST00000360190.8",
"protein_id": "ENSP00000353317.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1814,
"cds_start": -4,
"cds_end": null,
"cds_length": 5445,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5985,
"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": 39,
"intron_rank": 38,
"intron_rank_end": null,
"gene_symbol": "CDK5RAP2",
"gene_hgnc_id": 18672,
"hgvs_c": "n.*4450-80C>T",
"hgvs_p": null,
"transcript": "ENST00000473282.6",
"protein_id": "ENSP00000419265.1",
"transcript_support_level": 1,
"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": 38,
"intron_rank": 37,
"intron_rank_end": null,
"gene_symbol": "CDK5RAP2",
"gene_hgnc_id": 18672,
"hgvs_c": "n.*3453-80C>T",
"hgvs_p": null,
"transcript": "ENST00000480112.5",
"protein_id": "ENSP00000418418.1",
"transcript_support_level": 1,
"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": 5826,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CDK5RAP2",
"gene_hgnc_id": 18672,
"hgvs_c": "n.3050-80C>T",
"hgvs_p": null,
"transcript": "ENST00000484546.2",
"protein_id": null,
"transcript_support_level": 1,
"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": 3438,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDK5RAP2",
"gene_hgnc_id": 18672,
"hgvs_c": "c.*294C>T",
"hgvs_p": null,
"transcript": "ENST00000693728.1",
"protein_id": "ENSP00000510580.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1867,
"cds_start": -4,
"cds_end": null,
"cds_length": 5604,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6071,
"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": 38,
"intron_rank": 37,
"intron_rank_end": null,
"gene_symbol": "CDK5RAP2",
"gene_hgnc_id": 18672,
"hgvs_c": "c.5623-80C>T",
"hgvs_p": null,
"transcript": "NM_001410994.1",
"protein_id": "NP_001397923.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1892,
"cds_start": -4,
"cds_end": null,
"cds_length": 5679,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6229,
"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": 38,
"intron_rank": 37,
"intron_rank_end": null,
"gene_symbol": "CDK5RAP2",
"gene_hgnc_id": 18672,
"hgvs_c": "c.5623-80C>T",
"hgvs_p": null,
"transcript": "ENST00000687279.1",
"protein_id": "ENSP00000508692.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1892,
"cds_start": -4,
"cds_end": null,
"cds_length": 5679,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6079,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": 36,
"intron_rank_end": null,
"gene_symbol": "CDK5RAP2",
"gene_hgnc_id": 18672,
"hgvs_c": "c.5530-80C>T",
"hgvs_p": null,
"transcript": "NM_001410993.1",
"protein_id": "NP_001397922.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1861,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"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": 37,
"intron_rank": 36,
"intron_rank_end": null,
"gene_symbol": "CDK5RAP2",
"gene_hgnc_id": 18672,
"hgvs_c": "c.5530-80C>T",
"hgvs_p": null,
"transcript": "ENST00000416449.6",
"protein_id": "ENSP00000400395.2",
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
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"gene_symbol": "CDK5RAP2",
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"hgvs_c": "c.5527-80C>T",
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"transcript": "NM_001410992.1",
"protein_id": "NP_001397921.1",
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"feature": null
},
{
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"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"intron_rank": 36,
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"gene_symbol": "CDK5RAP2",
"gene_hgnc_id": 18672,
"hgvs_c": "c.5527-80C>T",
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"transcript": "ENST00000687633.1",
"protein_id": "ENSP00000510289.1",
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},
{
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"strand": false,
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],
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"intron_rank": 35,
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"gene_symbol": "CDK5RAP2",
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},
{
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],
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"gene_symbol": "CDK5RAP2",
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"hgvs_c": "c.5389-80C>T",
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"transcript": "NM_001011649.3",
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},
{
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],
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"gene_symbol": "CDK5RAP2",
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"hgvs_c": "c.4936-80C>T",
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"transcript": "NM_001272039.2",
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},
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],
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"gene_symbol": "CDK5RAP2",
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"transcript": "ENST00000360822.8",
"protein_id": "ENSP00000354065.4",
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},
{
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],
"exon_rank": null,
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"intron_rank": 15,
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"gene_symbol": "CDK5RAP2",
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"hgvs_c": "c.2656-80C>T",
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"transcript": "ENST00000425647.1",
"protein_id": "ENSP00000409941.1",
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},
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],
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"gene_symbol": "CDK5RAP2",
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"hgvs_c": "c.1234-80C>T",
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},
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],
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},
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],
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},
{
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"strand": false,
"consequences": [
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],
"exon_rank": null,
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"intron_rank": 22,
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"gene_symbol": "CDK5RAP2",
"gene_hgnc_id": 18672,
"hgvs_c": "n.3873-80C>T",
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"transcript": "ENST00000479584.2",
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"feature": null
},
{
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"protein_coding": false,
"strand": false,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CDK5RAP2",
"gene_hgnc_id": 18672,
"hgvs_c": "n.838-80C>T",
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"transcript": "ENST00000480467.5",
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"feature": null
},
{
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],
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"gene_symbol": "CDK5RAP2",
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"transcript": "XM_047423589.1",
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},
{
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],
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"gene_symbol": "CDK5RAP2",
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"transcript": "XM_006717185.2",
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},
{
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"intron_variant"
],
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"gene_symbol": "CDK5RAP2",
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"transcript": "XM_047423590.1",
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},
{
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"intron_variant"
],
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"gene_symbol": "CDK5RAP2",
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"feature": null
}
],
"gene_symbol": "CDK5RAP2",
"gene_hgnc_id": 18672,
"dbsnp": "rs76452024",
"frequency_reference_population": 0.0021539622,
"hom_count_reference_population": 43,
"allele_count_reference_population": 2401,
"gnomad_exomes_af": 0.00114816,
"gnomad_genomes_af": 0.00851075,
"gnomad_exomes_ac": 1105,
"gnomad_genomes_ac": 1296,
"gnomad_exomes_homalt": 22,
"gnomad_genomes_homalt": 21,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9300000071525574,
"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": -0.93,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.748,
"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": -14,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS1,BS2",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_018249.6",
"gene_symbol": "CDK5RAP2",
"hgnc_id": 18672,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.5626-80C>T",
"hgvs_p": null
},
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000776055.1",
"gene_symbol": "ENSG00000301087",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.413+1462G>A",
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}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}