← Back to variant description
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: 9-109436926-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=109436926&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 109436926,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000374541.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.632C>T",
"hgvs_p": "p.Ala211Val",
"transcript": "NM_002829.4",
"protein_id": "NP_002820.3",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 913,
"cds_start": 632,
"cds_end": null,
"cds_length": 2742,
"cdna_start": 738,
"cdna_end": null,
"cdna_length": 6704,
"mane_select": "ENST00000374541.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.632C>T",
"hgvs_p": "p.Ala211Val",
"transcript": "ENST00000374541.4",
"protein_id": "ENSP00000363667.1",
"transcript_support_level": 5,
"aa_start": 211,
"aa_end": null,
"aa_length": 913,
"cds_start": 632,
"cds_end": null,
"cds_length": 2742,
"cdna_start": 738,
"cdna_end": null,
"cdna_length": 6704,
"mane_select": "NM_002829.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.239C>T",
"hgvs_p": "p.Ala80Val",
"transcript": "ENST00000412145.5",
"protein_id": "ENSP00000416654.1",
"transcript_support_level": 1,
"aa_start": 80,
"aa_end": null,
"aa_length": 782,
"cds_start": 239,
"cds_end": null,
"cds_length": 2349,
"cdna_start": 2793,
"cdna_end": null,
"cdna_length": 8765,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.239C>T",
"hgvs_p": "p.Ala80Val",
"transcript": "ENST00000446349.5",
"protein_id": "ENSP00000395384.1",
"transcript_support_level": 1,
"aa_start": 80,
"aa_end": null,
"aa_length": 737,
"cds_start": 239,
"cds_end": null,
"cds_length": 2214,
"cdna_start": 2793,
"cdna_end": null,
"cdna_length": 8630,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.632C>T",
"hgvs_p": "p.Ala211Val",
"transcript": "NM_001145368.2",
"protein_id": "NP_001138840.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 868,
"cds_start": 632,
"cds_end": null,
"cds_length": 2607,
"cdna_start": 738,
"cdna_end": null,
"cdna_length": 6569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.632C>T",
"hgvs_p": "p.Ala211Val",
"transcript": "ENST00000262539.7",
"protein_id": "ENSP00000262539.4",
"transcript_support_level": 5,
"aa_start": 211,
"aa_end": null,
"aa_length": 839,
"cds_start": 632,
"cds_end": null,
"cds_length": 2520,
"cdna_start": 744,
"cdna_end": null,
"cdna_length": 6832,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.239C>T",
"hgvs_p": "p.Ala80Val",
"transcript": "NM_001145369.2",
"protein_id": "NP_001138841.1",
"transcript_support_level": null,
"aa_start": 80,
"aa_end": null,
"aa_length": 782,
"cds_start": 239,
"cds_end": null,
"cds_length": 2349,
"cdna_start": 2793,
"cdna_end": null,
"cdna_length": 8759,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.239C>T",
"hgvs_p": "p.Ala80Val",
"transcript": "NM_001145370.2",
"protein_id": "NP_001138842.1",
"transcript_support_level": null,
"aa_start": 80,
"aa_end": null,
"aa_length": 737,
"cds_start": 239,
"cds_end": null,
"cds_length": 2214,
"cdna_start": 2793,
"cdna_end": null,
"cdna_length": 8624,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.695C>T",
"hgvs_p": "p.Ala232Val",
"transcript": "XM_011518888.3",
"protein_id": "XP_011517190.1",
"transcript_support_level": null,
"aa_start": 232,
"aa_end": null,
"aa_length": 934,
"cds_start": 695,
"cds_end": null,
"cds_length": 2805,
"cdna_start": 839,
"cdna_end": null,
"cdna_length": 6805,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.812C>T",
"hgvs_p": "p.Ala271Val",
"transcript": "XM_047423635.1",
"protein_id": "XP_047279591.1",
"transcript_support_level": null,
"aa_start": 271,
"aa_end": null,
"aa_length": 928,
"cds_start": 812,
"cds_end": null,
"cds_length": 2787,
"cdna_start": 916,
"cdna_end": null,
"cdna_length": 6747,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.665C>T",
"hgvs_p": "p.Ala222Val",
"transcript": "XM_047423636.1",
"protein_id": "XP_047279592.1",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 924,
"cds_start": 665,
"cds_end": null,
"cds_length": 2775,
"cdna_start": 4674,
"cdna_end": null,
"cdna_length": 10640,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.632C>T",
"hgvs_p": "p.Ala211Val",
"transcript": "XM_006717199.4",
"protein_id": "XP_006717262.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 913,
"cds_start": 632,
"cds_end": null,
"cds_length": 2742,
"cdna_start": 923,
"cdna_end": null,
"cdna_length": 6889,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.632C>T",
"hgvs_p": "p.Ala211Val",
"transcript": "XM_017014955.2",
"protein_id": "XP_016870444.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 913,
"cds_start": 632,
"cds_end": null,
"cds_length": 2742,
"cdna_start": 6231,
"cdna_end": null,
"cdna_length": 12197,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.632C>T",
"hgvs_p": "p.Ala211Val",
"transcript": "XM_047423634.1",
"protein_id": "XP_047279590.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 913,
"cds_start": 632,
"cds_end": null,
"cds_length": 2742,
"cdna_start": 710,
"cdna_end": null,
"cdna_length": 6676,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.665C>T",
"hgvs_p": "p.Ala222Val",
"transcript": "XM_047423637.1",
"protein_id": "XP_047279593.1",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 879,
"cds_start": 665,
"cds_end": null,
"cds_length": 2640,
"cdna_start": 853,
"cdna_end": null,
"cdna_length": 6684,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.305C>T",
"hgvs_p": "p.Ala102Val",
"transcript": "XM_047423638.1",
"protein_id": "XP_047279594.1",
"transcript_support_level": null,
"aa_start": 102,
"aa_end": null,
"aa_length": 804,
"cds_start": 305,
"cds_end": null,
"cds_length": 2415,
"cdna_start": 364,
"cdna_end": null,
"cdna_length": 6330,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.287C>T",
"hgvs_p": "p.Ala96Val",
"transcript": "XM_006717202.4",
"protein_id": "XP_006717265.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 798,
"cds_start": 287,
"cds_end": null,
"cds_length": 2397,
"cdna_start": 447,
"cdna_end": null,
"cdna_length": 6413,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.287C>T",
"hgvs_p": "p.Ala96Val",
"transcript": "XM_006717203.5",
"protein_id": "XP_006717266.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 798,
"cds_start": 287,
"cds_end": null,
"cds_length": 2397,
"cdna_start": 406,
"cdna_end": null,
"cdna_length": 6372,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"dbsnp": "rs193920798",
"frequency_reference_population": 0.00002973882,
"hom_count_reference_population": 1,
"allele_count_reference_population": 48,
"gnomad_exomes_af": 0.0000287322,
"gnomad_genomes_af": 0.0000394021,
"gnomad_exomes_ac": 42,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7019972801208496,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.686,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.5138,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.15,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.236,
"phylop100way_prediction": "Pathogenic",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000374541.4",
"gene_symbol": "PTPN3",
"hgnc_id": 9655,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown",
"hgvs_c": "c.632C>T",
"hgvs_p": "p.Ala211Val"
}
],
"clinvar_disease": "Prostate cancer",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Prostate cancer",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}