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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: 9-109424357-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=109424357&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 109424357,
"ref": "A",
"alt": "G",
"effect": "intron_variant",
"transcript": "ENST00000374541.4",
"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": 26,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1002-1505T>C",
"hgvs_p": null,
"transcript": "NM_002829.4",
"protein_id": "NP_002820.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 913,
"cds_start": -4,
"cds_end": null,
"cds_length": 2742,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6704,
"mane_select": "ENST00000374541.4",
"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": 26,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1002-1505T>C",
"hgvs_p": null,
"transcript": "ENST00000374541.4",
"protein_id": "ENSP00000363667.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 913,
"cds_start": -4,
"cds_end": null,
"cds_length": 2742,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6704,
"mane_select": "NM_002829.4",
"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": 21,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.609-1505T>C",
"hgvs_p": null,
"transcript": "ENST00000412145.5",
"protein_id": "ENSP00000416654.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 782,
"cds_start": -4,
"cds_end": null,
"cds_length": 2349,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8765,
"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": 7,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.608+2593T>C",
"hgvs_p": null,
"transcript": "ENST00000446349.5",
"protein_id": "ENSP00000395384.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 737,
"cds_start": -4,
"cds_end": null,
"cds_length": 2214,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8630,
"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": 12,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1001+2593T>C",
"hgvs_p": null,
"transcript": "NM_001145368.2",
"protein_id": "NP_001138840.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 868,
"cds_start": -4,
"cds_end": null,
"cds_length": 2607,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6569,
"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": 26,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1002-1505T>C",
"hgvs_p": null,
"transcript": "ENST00000262539.7",
"protein_id": "ENSP00000262539.4",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 839,
"cds_start": -4,
"cds_end": null,
"cds_length": 2520,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6832,
"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": 21,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.609-1505T>C",
"hgvs_p": null,
"transcript": "NM_001145369.2",
"protein_id": "NP_001138841.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 782,
"cds_start": -4,
"cds_end": null,
"cds_length": 2349,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8759,
"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": 7,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.608+2593T>C",
"hgvs_p": null,
"transcript": "NM_001145370.2",
"protein_id": "NP_001138842.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 737,
"cds_start": -4,
"cds_end": null,
"cds_length": 2214,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8624,
"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": 2,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.141-1505T>C",
"hgvs_p": null,
"transcript": "NM_001145371.2",
"protein_id": "NP_001138843.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 626,
"cds_start": -4,
"cds_end": null,
"cds_length": 1881,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6122,
"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": 2,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.140+2593T>C",
"hgvs_p": null,
"transcript": "NM_001145372.2",
"protein_id": "NP_001138844.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 581,
"cds_start": -4,
"cds_end": null,
"cds_length": 1746,
"cdna_start": null,
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"cdna_length": 5987,
"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": 26,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1065-1505T>C",
"hgvs_p": null,
"transcript": "XM_011518888.3",
"protein_id": "XP_011517190.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 934,
"cds_start": -4,
"cds_end": null,
"cds_length": 2805,
"cdna_start": null,
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"cdna_length": 6805,
"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,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1181+2593T>C",
"hgvs_p": null,
"transcript": "XM_047423635.1",
"protein_id": "XP_047279591.1",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"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": 28,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1035-1505T>C",
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"transcript": "XM_047423636.1",
"protein_id": "XP_047279592.1",
"transcript_support_level": null,
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},
{
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"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 26,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1002-1505T>C",
"hgvs_p": null,
"transcript": "XM_006717199.4",
"protein_id": "XP_006717262.1",
"transcript_support_level": null,
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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": 26,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1002-1505T>C",
"hgvs_p": null,
"transcript": "XM_017014955.2",
"protein_id": "XP_016870444.1",
"transcript_support_level": null,
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"mane_select": null,
"mane_plus": null,
"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": 26,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1002-1505T>C",
"hgvs_p": null,
"transcript": "XM_047423634.1",
"protein_id": "XP_047279590.1",
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},
{
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"intron_variant"
],
"exon_rank": null,
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"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1034+2593T>C",
"hgvs_p": null,
"transcript": "XM_047423637.1",
"protein_id": "XP_047279593.1",
"transcript_support_level": null,
"aa_start": 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": 23,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.675-1505T>C",
"hgvs_p": null,
"transcript": "XM_047423638.1",
"protein_id": "XP_047279594.1",
"transcript_support_level": null,
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},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.657-1505T>C",
"hgvs_p": null,
"transcript": "XM_006717202.4",
"protein_id": "XP_006717265.1",
"transcript_support_level": null,
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},
{
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"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 23,
"intron_rank": 9,
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"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.657-1505T>C",
"hgvs_p": null,
"transcript": "XM_006717203.5",
"protein_id": "XP_006717266.1",
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"feature": null
}
],
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"dbsnp": "rs10521094",
"frequency_reference_population": 0.0298629,
"hom_count_reference_population": 121,
"allele_count_reference_population": 4548,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.0298629,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 4548,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 121,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8700000047683716,
"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": -0.87,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.661,
"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": "ENST00000374541.4",
"gene_symbol": "PTPN3",
"hgnc_id": 9655,
"effects": [
"intron_variant"
],
"inheritance_mode": "Unknown",
"hgvs_c": "c.1002-1505T>C",
"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
}