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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: 18-12821594-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=12821594&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "18",
"pos": 12821594,
"ref": "A",
"alt": "G",
"effect": "intron_variant",
"transcript": "ENST00000309660.10",
"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": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.495+4216T>C",
"hgvs_p": null,
"transcript": "NM_002828.4",
"protein_id": "NP_002819.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 415,
"cds_start": -4,
"cds_end": null,
"cds_length": 1248,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3470,
"mane_select": "ENST00000309660.10",
"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": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.495+4216T>C",
"hgvs_p": null,
"transcript": "ENST00000309660.10",
"protein_id": "ENSP00000311857.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 415,
"cds_start": -4,
"cds_end": null,
"cds_length": 1248,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3470,
"mane_select": "NM_002828.4",
"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": 11,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.496-2312T>C",
"hgvs_p": null,
"transcript": "ENST00000591115.5",
"protein_id": "ENSP00000466936.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 410,
"cds_start": -4,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1648,
"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": 10,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.495+4216T>C",
"hgvs_p": null,
"transcript": "ENST00000327283.7",
"protein_id": "ENSP00000320298.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 387,
"cds_start": -4,
"cds_end": null,
"cds_length": 1164,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1706,
"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": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.495+4216T>C",
"hgvs_p": null,
"transcript": "ENST00000353319.8",
"protein_id": "ENSP00000320546.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 353,
"cds_start": -4,
"cds_end": null,
"cds_length": 1062,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1542,
"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": 11,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.496-2312T>C",
"hgvs_p": null,
"transcript": "NM_001207013.2",
"protein_id": "NP_001193942.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 410,
"cds_start": -4,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1674,
"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": 10,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.495+4216T>C",
"hgvs_p": null,
"transcript": "NM_080422.3",
"protein_id": "NP_536347.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 387,
"cds_start": -4,
"cds_end": null,
"cds_length": 1164,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1605,
"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": 8,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.408+4216T>C",
"hgvs_p": null,
"transcript": "NM_001308287.1",
"protein_id": "NP_001295216.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 386,
"cds_start": -4,
"cds_end": null,
"cds_length": 1161,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3313,
"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": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.408+4216T>C",
"hgvs_p": null,
"transcript": "ENST00000591497.5",
"protein_id": "ENSP00000467823.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 386,
"cds_start": -4,
"cds_end": null,
"cds_length": 1161,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3390,
"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": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.495+4216T>C",
"hgvs_p": null,
"transcript": "NM_080423.3",
"protein_id": "NP_536348.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 353,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"cdna_length": 1503,
"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": 11,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.198+4216T>C",
"hgvs_p": null,
"transcript": "ENST00000645191.1",
"protein_id": "ENSP00000493693.1",
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"cds_start": -4,
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},
{
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"strand": false,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 10,
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"gene_symbol": "PTPN2",
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"hgvs_c": "c.198+4216T>C",
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"transcript": "ENST00000646492.1",
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},
{
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"strand": false,
"consequences": [
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],
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"gene_symbol": "PTPN2",
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"hgvs_c": "c.132+9349T>C",
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"transcript": "ENST00000587703.5",
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},
{
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"strand": false,
"consequences": [
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],
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"gene_symbol": "PTPN2",
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"hgvs_c": "n.*275+4216T>C",
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"transcript": "ENST00000589216.1",
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},
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],
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"transcript": "ENST00000591305.5",
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},
{
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"strand": false,
"consequences": [
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],
"exon_rank": null,
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"intron_rank": 5,
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"gene_symbol": "PTPN2",
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"hgvs_c": "n.495+4216T>C",
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"transcript": "ENST00000592776.1",
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},
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],
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"gene_symbol": "PTPN2",
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"hgvs_c": "n.496-169T>C",
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"transcript": "ENST00000645816.1",
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},
{
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"strand": false,
"consequences": [
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],
"exon_rank": null,
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"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
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"hgvs_c": "c.748-2312T>C",
"hgvs_p": null,
"transcript": "XM_047437695.1",
"protein_id": "XP_047293651.1",
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],
"exon_rank": null,
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"exon_count": 12,
"intron_rank": 6,
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"gene_symbol": "PTPN2",
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"hgvs_c": "c.747+4216T>C",
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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_variant"
],
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"exon_count": 10,
"intron_rank": 5,
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"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.408+4216T>C",
"hgvs_p": null,
"transcript": "XM_047437697.1",
"protein_id": "XP_047293653.1",
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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": 9,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PTPN2",
"gene_hgnc_id": 9650,
"hgvs_c": "c.361-4229T>C",
"hgvs_p": null,
"transcript": "XM_024451228.2",
"protein_id": "XP_024306996.1",
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}
],
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"dbsnp": "rs2847281",
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"hom_count_reference_population": 8935,
"allele_count_reference_population": 48104,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.31612,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 48104,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 8935,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7799999713897705,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.78,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.306,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": "ENST00000309660.10",
"gene_symbol": "PTPN2",
"hgnc_id": 9650,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.495+4216T>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
}