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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: 9-8331574-A-AAACTTACCATTCTTGAACTGT (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=8331574&ref=A&alt=AAACTTACCATTCTTGAACTGT&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 8331574,
"ref": "A",
"alt": "AAACTTACCATTCTTGAACTGT",
"effect": "splice_region_variant,intron_variant",
"transcript": "NM_002839.4",
"consequences": [
{
"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": 46,
"intron_rank": 44,
"intron_rank_end": null,
"gene_symbol": "PTPRD",
"gene_hgnc_id": 9668,
"hgvs_c": "c.5534+7_5534+8insACAGTTCAAGAATGGTAAGTT",
"hgvs_p": null,
"transcript": "NM_002839.4",
"protein_id": "NP_002830.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1912,
"cds_start": -4,
"cds_end": null,
"cds_length": 5739,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10389,
"mane_select": "ENST00000381196.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 46,
"intron_rank": 44,
"intron_rank_end": null,
"gene_symbol": "PTPRD",
"gene_hgnc_id": 9668,
"hgvs_c": "c.5534+7_5534+8insACAGTTCAAGAATGGTAAGTT",
"hgvs_p": null,
"transcript": "ENST00000381196.9",
"protein_id": "ENSP00000370593.3",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1912,
"cds_start": -4,
"cds_end": null,
"cds_length": 5739,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10389,
"mane_select": "NM_002839.4",
"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": 31,
"intron_rank": 29,
"intron_rank_end": null,
"gene_symbol": "PTPRD",
"gene_hgnc_id": 9668,
"hgvs_c": "c.4316+7_4316+8insACAGTTCAAGAATGGTAAGTT",
"hgvs_p": null,
"transcript": "ENST00000355233.9",
"protein_id": "ENSP00000347373.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1506,
"cds_start": -4,
"cds_end": null,
"cds_length": 4521,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8251,
"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": 29,
"intron_rank": 27,
"intron_rank_end": null,
"gene_symbol": "PTPRD",
"gene_hgnc_id": 9668,
"hgvs_c": "c.4313+7_4313+8insACAGTTCAAGAATGGTAAGTT",
"hgvs_p": null,
"transcript": "ENST00000397606.7",
"protein_id": "ENSP00000380731.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1505,
"cds_start": -4,
"cds_end": null,
"cds_length": 4518,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5038,
"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": 31,
"intron_rank": 29,
"intron_rank_end": null,
"gene_symbol": "PTPRD",
"gene_hgnc_id": 9668,
"hgvs_c": "c.4313+7_4313+8insACAGTTCAAGAATGGTAAGTT",
"hgvs_p": null,
"transcript": "ENST00000486161.5",
"protein_id": "ENSP00000417093.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1505,
"cds_start": -4,
"cds_end": null,
"cds_length": 4518,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5039,
"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": 29,
"intron_rank": 27,
"intron_rank_end": null,
"gene_symbol": "PTPRD",
"gene_hgnc_id": 9668,
"hgvs_c": "c.4286+7_4286+8insACAGTTCAAGAATGGTAAGTT",
"hgvs_p": null,
"transcript": "ENST00000537002.5",
"protein_id": "ENSP00000440515.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1496,
"cds_start": -4,
"cds_end": null,
"cds_length": 4491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8224,
"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": 38,
"intron_rank": 36,
"intron_rank_end": null,
"gene_symbol": "PTPRD",
"gene_hgnc_id": 9668,
"hgvs_c": "c.5594+7_5594+8insACAGTTCAAGAATGGTAAGTT",
"hgvs_p": null,
"transcript": "NM_001377958.1",
"protein_id": "NP_001364887.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1932,
"cds_start": -4,
"cds_end": null,
"cds_length": 5799,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9760,
"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": 37,
"intron_rank": 35,
"intron_rank_end": null,
"gene_symbol": "PTPRD",
"gene_hgnc_id": 9668,
"hgvs_c": "c.5549+7_5549+8insACAGTTCAAGAATGGTAAGTT",
"hgvs_p": null,
"transcript": "NM_001378058.1",
"protein_id": "NP_001364987.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1917,
"cds_start": -4,
"cds_end": null,
"cds_length": 5754,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9715,
"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": 35,
"intron_rank": 33,
"intron_rank_end": null,
"gene_symbol": "PTPRD",
"gene_hgnc_id": 9668,
"hgvs_c": "c.5534+7_5534+8insACAGTTCAAGAATGGTAAGTT",
"hgvs_p": null,
"transcript": "ENST00000356435.9",
"protein_id": "ENSP00000348812.5",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1912,
"cds_start": -4,
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"cds_length": 5739,
"cdna_start": null,
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"cdna_length": 9472,
"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": 36,
"intron_rank": 33,
"intron_rank_end": null,
"gene_symbol": "PTPRD",
"gene_hgnc_id": 9668,
"hgvs_c": "c.5534+7_5534+8insACAGTTCAAGAATGGTAAGTT",
"hgvs_p": null,
"transcript": "ENST00000540109.5",
"protein_id": "ENSP00000438164.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1912,
"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": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": 46,
"intron_rank_end": null,
"gene_symbol": "PTPRD",
"gene_hgnc_id": 9668,
"hgvs_c": "c.5534+7_5534+8insACAGTTCAAGAATGGTAAGTT",
"hgvs_p": null,
"transcript": "ENST00000850942.1",
"protein_id": "ENSP00000521027.1",
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"aa_start": null,
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"cds_start": -4,
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},
{
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"strand": false,
"consequences": [
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"intron_variant"
],
"exon_rank": null,
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"exon_count": 31,
"intron_rank": 29,
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"gene_symbol": "PTPRD",
"gene_hgnc_id": 9668,
"hgvs_c": "c.4325+7_4325+8insACAGTTCAAGAATGGTAAGTT",
"hgvs_p": null,
"transcript": "NM_001377946.1",
"protein_id": "NP_001364875.1",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": -4,
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},
{
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"strand": false,
"consequences": [
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"intron_variant"
],
"exon_rank": null,
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"exon_count": 29,
"intron_rank": 27,
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"gene_symbol": "PTPRD",
"gene_hgnc_id": 9668,
"hgvs_c": "c.4322+7_4322+8insACAGTTCAAGAATGGTAAGTT",
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"transcript": "ENST00000397617.8",
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},
{
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"intron_variant"
],
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"intron_rank": 29,
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"gene_symbol": "PTPRD",
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"transcript": "NM_130392.3",
"protein_id": "NP_569076.2",
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"aa_start": null,
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},
{
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"consequences": [
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],
"exon_rank": null,
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"exon_count": 30,
"intron_rank": 28,
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"gene_symbol": "PTPRD",
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"hgvs_c": "c.4313+7_4313+8insACAGTTCAAGAATGGTAAGTT",
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"transcript": "NM_001171025.2",
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},
{
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],
"exon_rank": null,
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"intron_rank": 30,
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"gene_symbol": "PTPRD",
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"hgvs_c": "c.4313+7_4313+8insACAGTTCAAGAATGGTAAGTT",
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"transcript": "NM_130391.4",
"protein_id": "NP_569075.2",
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},
{
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"consequences": [
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],
"exon_rank": null,
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"exon_count": 30,
"intron_rank": 28,
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"gene_symbol": "PTPRD",
"gene_hgnc_id": 9668,
"hgvs_c": "c.4304+7_4304+8insACAGTTCAAGAATGGTAAGTT",
"hgvs_p": null,
"transcript": "NM_001040712.2",
"protein_id": "NP_001035802.1",
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},
{
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"intron_variant"
],
"exon_rank": null,
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"exon_count": 30,
"intron_rank": 28,
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"transcript": "ENST00000397611.7",
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"intron_variant"
],
"exon_rank": null,
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"intron_rank": 28,
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"gene_symbol": "PTPRD",
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"hgvs_c": "c.4295+7_4295+8insACAGTTCAAGAATGGTAAGTT",
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"transcript": "NM_001377947.1",
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},
{
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],
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"gene_symbol": "PTPRD",
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"hgvs_c": "c.4286+7_4286+8insACAGTTCAAGAATGGTAAGTT",
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"transcript": "NM_130393.3",
"protein_id": "NP_569077.2",
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"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": 30,
"intron_rank": 28,
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"gene_symbol": "PTPRD",
"gene_hgnc_id": 9668,
"hgvs_c": "n.4912+7_4912+8insACAGTTCAAGAATGGTAAGTT",
"hgvs_p": null,
"transcript": "ENST00000651105.1",
"protein_id": null,
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"mane_select": null,
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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"intron_variant"
],
"exon_rank": null,
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"exon_count": 47,
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"gnomad_genomes_af": 0.296057,
"gnomad_exomes_ac": 246601,
"gnomad_genomes_ac": 44987,
"gnomad_exomes_homalt": 26822,
"gnomad_genomes_homalt": 10516,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 0.111,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP6_Moderate,BA1",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP6_Moderate",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_002839.4",
"gene_symbol": "PTPRD",
"hgnc_id": 9668,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.5534+7_5534+8insACAGTTCAAGAATGGTAAGTT",
"hgvs_p": null
}
],
"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
}