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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: 1-113829710-T-TA (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=113829710&ref=T&alt=TA&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 113829710,
"ref": "T",
"alt": "TA",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000359785.10",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.2135-4_2135-3insT",
"hgvs_p": null,
"transcript": "ENST00000359785.10",
"protein_id": "ENSP00000352833.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 807,
"cds_start": -4,
"cds_end": null,
"cds_length": 2424,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3607,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.2135-4_2135-3insT",
"hgvs_p": null,
"transcript": "ENST00000420377.6",
"protein_id": "ENSP00000388229.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 795,
"cds_start": -4,
"cds_end": null,
"cds_length": 2388,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2726,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.2063-4_2063-3insT",
"hgvs_p": null,
"transcript": "ENST00000538253.5",
"protein_id": "ENSP00000439372.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 783,
"cds_start": -4,
"cds_end": null,
"cds_length": 2352,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3575,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.1970-4_1970-3insT",
"hgvs_p": null,
"transcript": "ENST00000528414.5",
"protein_id": "ENSP00000435176.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 752,
"cds_start": -4,
"cds_end": null,
"cds_length": 2259,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3424,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.1754-4_1754-3insT",
"hgvs_p": null,
"transcript": "ENST00000525799.1",
"protein_id": "ENSP00000432674.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 668,
"cds_start": -4,
"cds_end": null,
"cds_length": 2007,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2118,
"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": 6,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.469-10057_469-10056insT",
"hgvs_p": null,
"transcript": "ENST00000460620.5",
"protein_id": "ENSP00000433141.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 179,
"cds_start": -4,
"cds_end": null,
"cds_length": 540,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1794,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.2135-4dupT",
"hgvs_p": null,
"transcript": "NM_015967.8",
"protein_id": "NP_057051.4",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 807,
"cds_start": -4,
"cds_end": null,
"cds_length": 2424,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3607,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.2063-4dupT",
"hgvs_p": null,
"transcript": "NM_001308297.2",
"protein_id": "NP_001295226.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 783,
"cds_start": -4,
"cds_end": null,
"cds_length": 2352,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3535,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.2051-4dupT",
"hgvs_p": null,
"transcript": "NM_001193431.3",
"protein_id": "NP_001180360.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 779,
"cds_start": -4,
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"cds_length": 2340,
"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": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.1970-4dupT",
"hgvs_p": null,
"transcript": "NM_012411.6",
"protein_id": "NP_036543.5",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
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"cds_start": -4,
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"cds_length": 2259,
"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": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
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"exon_count": 17,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "n.*1413-4_*1413-3insT",
"hgvs_p": null,
"transcript": "ENST00000532224.5",
"protein_id": "ENSP00000431249.1",
"transcript_support_level": 2,
"aa_start": null,
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"cds_start": -4,
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},
{
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],
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"intron_rank": 3,
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"transcript": "ENST00000664434.1",
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},
{
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"strand": true,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 6,
"intron_rank": 3,
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"gene_symbol": "AP4B1-AS1",
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"hgvs_c": "n.440+14238_440+14239insA",
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},
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"strand": true,
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],
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],
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"gene_symbol": "AP4B1-AS1",
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"hgvs_c": "n.414+14250dupA",
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"transcript": "NR_125965.1",
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},
{
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"intron_variant"
],
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"exon_count": 20,
"intron_rank": 16,
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"gene_symbol": "PTPN22",
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"hgvs_c": "c.2057-4dupT",
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"transcript": "XM_011541221.2",
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},
{
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],
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"hgvs_c": "c.2135-4dupT",
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"protein_id": "XP_011539524.1",
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},
{
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"strand": false,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 19,
"intron_rank": 15,
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"gene_symbol": "PTPN22",
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"hgvs_c": "c.1985-4dupT",
"hgvs_p": null,
"transcript": "XM_047417630.1",
"protein_id": "XP_047273586.1",
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},
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],
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],
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},
{
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],
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"hgvs_c": "c.1790-4dupT",
"hgvs_p": null,
"transcript": "XM_017001005.3",
"protein_id": "XP_016856494.1",
"transcript_support_level": null,
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"aa_length": 692,
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"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTPN22",
"gene_hgnc_id": 9652,
"dbsnp": "rs57877024",
"frequency_reference_population": 0.014408023,
"hom_count_reference_population": 0,
"allele_count_reference_population": 17946,
"gnomad_exomes_af": 0.0163243,
"gnomad_genomes_af": 0.0001087,
"gnomad_exomes_ac": 17930,
"gnomad_genomes_ac": 16,
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"gnomad_genomes_homalt": 0,
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"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 1.679,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000359785.10",
"gene_symbol": "PTPN22",
"hgnc_id": 9652,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "Unknown,AR",
"hgvs_c": "c.2135-4_2135-3insT",
"hgvs_p": null
},
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "NR_125965.1",
"gene_symbol": "AP4B1-AS1",
"hgnc_id": 44114,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.414+14250dupA",
"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
}