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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: 2-132989057-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=132989057&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 132989057,
"ref": "A",
"alt": "C",
"effect": "intron_variant",
"transcript": "ENST00000409261.6",
"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": 20,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "NCKAP5",
"gene_hgnc_id": 29847,
"hgvs_c": "c.429+5095T>G",
"hgvs_p": null,
"transcript": "NM_207363.3",
"protein_id": "NP_997246.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1909,
"cds_start": -4,
"cds_end": null,
"cds_length": 5730,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7608,
"mane_select": "ENST00000409261.6",
"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": 20,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "NCKAP5",
"gene_hgnc_id": 29847,
"hgvs_c": "c.429+5095T>G",
"hgvs_p": null,
"transcript": "ENST00000409261.6",
"protein_id": "ENSP00000387128.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1909,
"cds_start": -4,
"cds_end": null,
"cds_length": 5730,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7608,
"mane_select": "NM_207363.3",
"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": 18,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "NCKAP5",
"gene_hgnc_id": 29847,
"hgvs_c": "c.429+5095T>G",
"hgvs_p": null,
"transcript": "NM_207481.4",
"protein_id": "NP_997364.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 590,
"cds_start": -4,
"cds_end": null,
"cds_length": 1773,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3651,
"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": 18,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "NCKAP5",
"gene_hgnc_id": 29847,
"hgvs_c": "c.429+5095T>G",
"hgvs_p": null,
"transcript": "ENST00000409213.5",
"protein_id": "ENSP00000386952.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 590,
"cds_start": -4,
"cds_end": null,
"cds_length": 1773,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2390,
"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": 18,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "NCKAP5",
"gene_hgnc_id": 29847,
"hgvs_c": "c.429+5095T>G",
"hgvs_p": null,
"transcript": "XM_005263659.5",
"protein_id": "XP_005263716.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1953,
"cds_start": -4,
"cds_end": null,
"cds_length": 5862,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7407,
"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": 18,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "NCKAP5",
"gene_hgnc_id": 29847,
"hgvs_c": "c.429+5095T>G",
"hgvs_p": null,
"transcript": "XM_005263660.5",
"protein_id": "XP_005263717.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1953,
"cds_start": -4,
"cds_end": null,
"cds_length": 5862,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7380,
"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": 20,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "NCKAP5",
"gene_hgnc_id": 29847,
"hgvs_c": "c.429+5095T>G",
"hgvs_p": null,
"transcript": "XM_011511097.4",
"protein_id": "XP_011509399.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1953,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"cdna_length": 7595,
"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": 19,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "NCKAP5",
"gene_hgnc_id": 29847,
"hgvs_c": "c.429+5095T>G",
"hgvs_p": null,
"transcript": "XM_011511099.4",
"protein_id": "XP_011509401.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1953,
"cds_start": -4,
"cds_end": null,
"cds_length": 5862,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7448,
"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": 19,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "NCKAP5",
"gene_hgnc_id": 29847,
"hgvs_c": "c.429+5095T>G",
"hgvs_p": null,
"transcript": "XM_011511100.4",
"protein_id": "XP_011509402.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1953,
"cds_start": -4,
"cds_end": null,
"cds_length": 5862,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7390,
"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": 19,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "NCKAP5",
"gene_hgnc_id": 29847,
"hgvs_c": "c.429+5095T>G",
"hgvs_p": null,
"transcript": "XM_017003974.1",
"protein_id": "XP_016859463.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1953,
"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,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 6,
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"gene_symbol": "NCKAP5",
"gene_hgnc_id": 29847,
"hgvs_c": "c.429+5095T>G",
"hgvs_p": null,
"transcript": "XM_017003975.3",
"protein_id": "XP_016859464.1",
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},
{
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"strand": false,
"consequences": [
"intron_variant"
],
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"gene_symbol": "NCKAP5",
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"transcript": "XM_011511102.3",
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},
{
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"strand": false,
"consequences": [
"intron_variant"
],
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"exon_count": 17,
"intron_rank": 5,
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"gene_symbol": "NCKAP5",
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"hgvs_c": "c.354+5095T>G",
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"transcript": "XM_017003977.3",
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},
{
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"strand": false,
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],
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"intron_rank": 6,
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"gene_symbol": "NCKAP5",
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"hgvs_c": "c.354+5095T>G",
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"transcript": "XM_047444128.1",
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},
{
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],
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"gene_symbol": "NCKAP5",
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"transcript": "XM_047444129.1",
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},
{
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],
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"gene_symbol": "NCKAP5",
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],
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"gene_symbol": "NCKAP5",
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},
{
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"consequences": [
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],
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"gene_symbol": "NCKAP5",
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"transcript": "XM_047444130.1",
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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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"intron_rank": 6,
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"gene_symbol": "NCKAP5",
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}
],
"gene_symbol": "NCKAP5",
"gene_hgnc_id": 29847,
"dbsnp": "rs1437898",
"frequency_reference_population": 0.5618381,
"hom_count_reference_population": 24543,
"allele_count_reference_population": 85414,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.561838,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 85414,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 24543,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7900000214576721,
"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": -0.79,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.122,
"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": "ENST00000409261.6",
"gene_symbol": "NCKAP5",
"hgnc_id": 29847,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.429+5095T>G",
"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
}