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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: 9-109383485-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=109383485&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 109383485,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_002829.4",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2320T>A",
"hgvs_p": "p.Cys774Ser",
"transcript": "NM_002829.4",
"protein_id": "NP_002820.3",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 913,
"cds_start": 2320,
"cds_end": null,
"cds_length": 2742,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000374541.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002829.4"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2320T>A",
"hgvs_p": "p.Cys774Ser",
"transcript": "ENST00000374541.4",
"protein_id": "ENSP00000363667.1",
"transcript_support_level": 5,
"aa_start": 774,
"aa_end": null,
"aa_length": 913,
"cds_start": 2320,
"cds_end": null,
"cds_length": 2742,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002829.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000374541.4"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1927T>A",
"hgvs_p": "p.Cys643Ser",
"transcript": "ENST00000412145.5",
"protein_id": "ENSP00000416654.1",
"transcript_support_level": 1,
"aa_start": 643,
"aa_end": null,
"aa_length": 782,
"cds_start": 1927,
"cds_end": null,
"cds_length": 2349,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000412145.5"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1792T>A",
"hgvs_p": "p.Cys598Ser",
"transcript": "ENST00000446349.5",
"protein_id": "ENSP00000395384.1",
"transcript_support_level": 1,
"aa_start": 598,
"aa_end": null,
"aa_length": 737,
"cds_start": 1792,
"cds_end": null,
"cds_length": 2214,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000446349.5"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2320T>A",
"hgvs_p": "p.Cys774Ser",
"transcript": "ENST00000865411.1",
"protein_id": "ENSP00000535470.1",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 913,
"cds_start": 2320,
"cds_end": null,
"cds_length": 2742,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865411.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2320T>A",
"hgvs_p": "p.Cys774Ser",
"transcript": "ENST00000865412.1",
"protein_id": "ENSP00000535471.1",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 913,
"cds_start": 2320,
"cds_end": null,
"cds_length": 2742,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865412.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2320T>A",
"hgvs_p": "p.Cys774Ser",
"transcript": "ENST00000865413.1",
"protein_id": "ENSP00000535472.1",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 913,
"cds_start": 2320,
"cds_end": null,
"cds_length": 2742,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865413.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2320T>A",
"hgvs_p": "p.Cys774Ser",
"transcript": "ENST00000865415.1",
"protein_id": "ENSP00000535474.1",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 913,
"cds_start": 2320,
"cds_end": null,
"cds_length": 2742,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865415.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2320T>A",
"hgvs_p": "p.Cys774Ser",
"transcript": "ENST00000865416.1",
"protein_id": "ENSP00000535475.1",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 913,
"cds_start": 2320,
"cds_end": null,
"cds_length": 2742,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865416.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2320T>A",
"hgvs_p": "p.Cys774Ser",
"transcript": "ENST00000865417.1",
"protein_id": "ENSP00000535476.1",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 913,
"cds_start": 2320,
"cds_end": null,
"cds_length": 2742,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865417.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2242T>A",
"hgvs_p": "p.Cys748Ser",
"transcript": "ENST00000865410.1",
"protein_id": "ENSP00000535469.1",
"transcript_support_level": null,
"aa_start": 748,
"aa_end": null,
"aa_length": 887,
"cds_start": 2242,
"cds_end": null,
"cds_length": 2664,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865410.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2185T>A",
"hgvs_p": "p.Cys729Ser",
"transcript": "NM_001145368.2",
"protein_id": "NP_001138840.1",
"transcript_support_level": null,
"aa_start": 729,
"aa_end": null,
"aa_length": 868,
"cds_start": 2185,
"cds_end": null,
"cds_length": 2607,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145368.2"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2320T>A",
"hgvs_p": "p.Cys774Ser",
"transcript": "ENST00000262539.7",
"protein_id": "ENSP00000262539.4",
"transcript_support_level": 5,
"aa_start": 774,
"aa_end": null,
"aa_length": 839,
"cds_start": 2320,
"cds_end": null,
"cds_length": 2520,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000262539.7"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2020T>A",
"hgvs_p": "p.Cys674Ser",
"transcript": "ENST00000865414.1",
"protein_id": "ENSP00000535473.1",
"transcript_support_level": null,
"aa_start": 674,
"aa_end": null,
"aa_length": 813,
"cds_start": 2020,
"cds_end": null,
"cds_length": 2442,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865414.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1927T>A",
"hgvs_p": "p.Cys643Ser",
"transcript": "NM_001145369.2",
"protein_id": "NP_001138841.1",
"transcript_support_level": null,
"aa_start": 643,
"aa_end": null,
"aa_length": 782,
"cds_start": 1927,
"cds_end": null,
"cds_length": 2349,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145369.2"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1792T>A",
"hgvs_p": "p.Cys598Ser",
"transcript": "NM_001145370.2",
"protein_id": "NP_001138842.1",
"transcript_support_level": null,
"aa_start": 598,
"aa_end": null,
"aa_length": 737,
"cds_start": 1792,
"cds_end": null,
"cds_length": 2214,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145370.2"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1459T>A",
"hgvs_p": "p.Cys487Ser",
"transcript": "NM_001145371.2",
"protein_id": "NP_001138843.1",
"transcript_support_level": null,
"aa_start": 487,
"aa_end": null,
"aa_length": 626,
"cds_start": 1459,
"cds_end": null,
"cds_length": 1881,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145371.2"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1324T>A",
"hgvs_p": "p.Cys442Ser",
"transcript": "NM_001145372.2",
"protein_id": "NP_001138844.1",
"transcript_support_level": null,
"aa_start": 442,
"aa_end": null,
"aa_length": 581,
"cds_start": 1324,
"cds_end": null,
"cds_length": 1746,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145372.2"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2383T>A",
"hgvs_p": "p.Cys795Ser",
"transcript": "XM_011518888.3",
"protein_id": "XP_011517190.1",
"transcript_support_level": null,
"aa_start": 795,
"aa_end": null,
"aa_length": 934,
"cds_start": 2383,
"cds_end": null,
"cds_length": 2805,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011518888.3"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2365T>A",
"hgvs_p": "p.Cys789Ser",
"transcript": "XM_047423635.1",
"protein_id": "XP_047279591.1",
"transcript_support_level": null,
"aa_start": 789,
"aa_end": null,
"aa_length": 928,
"cds_start": 2365,
"cds_end": null,
"cds_length": 2787,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047423635.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2353T>A",
"hgvs_p": "p.Cys785Ser",
"transcript": "XM_047423636.1",
"protein_id": "XP_047279592.1",
"transcript_support_level": null,
"aa_start": 785,
"aa_end": null,
"aa_length": 924,
"cds_start": 2353,
"cds_end": null,
"cds_length": 2775,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047423636.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2320T>A",
"hgvs_p": "p.Cys774Ser",
"transcript": "XM_006717199.4",
"protein_id": "XP_006717262.1",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 913,
"cds_start": 2320,
"cds_end": null,
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"cdna_start": null,
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{
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"computational_prediction_selected": "Pathogenic",
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"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.85,
"revel_prediction": "Pathogenic",
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"bayesdelnoaf_score": 0.32,
"bayesdelnoaf_prediction": "Pathogenic",
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"phylop100way_prediction": "Pathogenic",
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"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
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"acmg_by_gene": [
{
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"criteria": [
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],
"verdict": "Uncertain_significance",
"transcript": "NM_002829.4",
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"effects": [
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],
"inheritance_mode": "Unknown",
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],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}