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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: 9-109389341-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=109389341&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 109389341,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_002829.4",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2145C>T",
"hgvs_p": "p.Ile715Ile",
"transcript": "NM_002829.4",
"protein_id": "NP_002820.3",
"transcript_support_level": null,
"aa_start": 715,
"aa_end": null,
"aa_length": 913,
"cds_start": 2145,
"cds_end": null,
"cds_length": 2742,
"cdna_start": 2251,
"cdna_end": null,
"cdna_length": 6704,
"mane_select": "ENST00000374541.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002829.4"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2145C>T",
"hgvs_p": "p.Ile715Ile",
"transcript": "ENST00000374541.4",
"protein_id": "ENSP00000363667.1",
"transcript_support_level": 5,
"aa_start": 715,
"aa_end": null,
"aa_length": 913,
"cds_start": 2145,
"cds_end": null,
"cds_length": 2742,
"cdna_start": 2251,
"cdna_end": null,
"cdna_length": 6704,
"mane_select": "NM_002829.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000374541.4"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1752C>T",
"hgvs_p": "p.Ile584Ile",
"transcript": "ENST00000412145.5",
"protein_id": "ENSP00000416654.1",
"transcript_support_level": 1,
"aa_start": 584,
"aa_end": null,
"aa_length": 782,
"cds_start": 1752,
"cds_end": null,
"cds_length": 2349,
"cdna_start": 4306,
"cdna_end": null,
"cdna_length": 8765,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000412145.5"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1617C>T",
"hgvs_p": "p.Ile539Ile",
"transcript": "ENST00000446349.5",
"protein_id": "ENSP00000395384.1",
"transcript_support_level": 1,
"aa_start": 539,
"aa_end": null,
"aa_length": 737,
"cds_start": 1617,
"cds_end": null,
"cds_length": 2214,
"cdna_start": 4171,
"cdna_end": null,
"cdna_length": 8630,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000446349.5"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2145C>T",
"hgvs_p": "p.Ile715Ile",
"transcript": "ENST00000865411.1",
"protein_id": "ENSP00000535470.1",
"transcript_support_level": null,
"aa_start": 715,
"aa_end": null,
"aa_length": 913,
"cds_start": 2145,
"cds_end": null,
"cds_length": 2742,
"cdna_start": 2324,
"cdna_end": null,
"cdna_length": 4238,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865411.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2145C>T",
"hgvs_p": "p.Ile715Ile",
"transcript": "ENST00000865412.1",
"protein_id": "ENSP00000535471.1",
"transcript_support_level": null,
"aa_start": 715,
"aa_end": null,
"aa_length": 913,
"cds_start": 2145,
"cds_end": null,
"cds_length": 2742,
"cdna_start": 2357,
"cdna_end": null,
"cdna_length": 4271,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865412.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2145C>T",
"hgvs_p": "p.Ile715Ile",
"transcript": "ENST00000865413.1",
"protein_id": "ENSP00000535472.1",
"transcript_support_level": null,
"aa_start": 715,
"aa_end": null,
"aa_length": 913,
"cds_start": 2145,
"cds_end": null,
"cds_length": 2742,
"cdna_start": 2432,
"cdna_end": null,
"cdna_length": 4346,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865413.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2145C>T",
"hgvs_p": "p.Ile715Ile",
"transcript": "ENST00000865415.1",
"protein_id": "ENSP00000535474.1",
"transcript_support_level": null,
"aa_start": 715,
"aa_end": null,
"aa_length": 913,
"cds_start": 2145,
"cds_end": null,
"cds_length": 2742,
"cdna_start": 2242,
"cdna_end": null,
"cdna_length": 4156,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865415.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2145C>T",
"hgvs_p": "p.Ile715Ile",
"transcript": "ENST00000865416.1",
"protein_id": "ENSP00000535475.1",
"transcript_support_level": null,
"aa_start": 715,
"aa_end": null,
"aa_length": 913,
"cds_start": 2145,
"cds_end": null,
"cds_length": 2742,
"cdna_start": 2461,
"cdna_end": null,
"cdna_length": 4385,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865416.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2145C>T",
"hgvs_p": "p.Ile715Ile",
"transcript": "ENST00000865417.1",
"protein_id": "ENSP00000535476.1",
"transcript_support_level": null,
"aa_start": 715,
"aa_end": null,
"aa_length": 913,
"cds_start": 2145,
"cds_end": null,
"cds_length": 2742,
"cdna_start": 2458,
"cdna_end": null,
"cdna_length": 4374,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865417.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2067C>T",
"hgvs_p": "p.Ile689Ile",
"transcript": "ENST00000865410.1",
"protein_id": "ENSP00000535469.1",
"transcript_support_level": null,
"aa_start": 689,
"aa_end": null,
"aa_length": 887,
"cds_start": 2067,
"cds_end": null,
"cds_length": 2664,
"cdna_start": 2199,
"cdna_end": null,
"cdna_length": 4100,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865410.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2010C>T",
"hgvs_p": "p.Ile670Ile",
"transcript": "NM_001145368.2",
"protein_id": "NP_001138840.1",
"transcript_support_level": null,
"aa_start": 670,
"aa_end": null,
"aa_length": 868,
"cds_start": 2010,
"cds_end": null,
"cds_length": 2607,
"cdna_start": 2116,
"cdna_end": null,
"cdna_length": 6569,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145368.2"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2145C>T",
"hgvs_p": "p.Ile715Ile",
"transcript": "ENST00000262539.7",
"protein_id": "ENSP00000262539.4",
"transcript_support_level": 5,
"aa_start": 715,
"aa_end": null,
"aa_length": 839,
"cds_start": 2145,
"cds_end": null,
"cds_length": 2520,
"cdna_start": 2257,
"cdna_end": null,
"cdna_length": 6832,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000262539.7"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1845C>T",
"hgvs_p": "p.Ile615Ile",
"transcript": "ENST00000865414.1",
"protein_id": "ENSP00000535473.1",
"transcript_support_level": null,
"aa_start": 615,
"aa_end": null,
"aa_length": 813,
"cds_start": 1845,
"cds_end": null,
"cds_length": 2442,
"cdna_start": 1916,
"cdna_end": null,
"cdna_length": 3833,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865414.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1752C>T",
"hgvs_p": "p.Ile584Ile",
"transcript": "NM_001145369.2",
"protein_id": "NP_001138841.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 782,
"cds_start": 1752,
"cds_end": null,
"cds_length": 2349,
"cdna_start": 4306,
"cdna_end": null,
"cdna_length": 8759,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145369.2"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1617C>T",
"hgvs_p": "p.Ile539Ile",
"transcript": "NM_001145370.2",
"protein_id": "NP_001138842.1",
"transcript_support_level": null,
"aa_start": 539,
"aa_end": null,
"aa_length": 737,
"cds_start": 1617,
"cds_end": null,
"cds_length": 2214,
"cdna_start": 4171,
"cdna_end": null,
"cdna_length": 8624,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145370.2"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1284C>T",
"hgvs_p": "p.Ile428Ile",
"transcript": "NM_001145371.2",
"protein_id": "NP_001138843.1",
"transcript_support_level": null,
"aa_start": 428,
"aa_end": null,
"aa_length": 626,
"cds_start": 1284,
"cds_end": null,
"cds_length": 1881,
"cdna_start": 1669,
"cdna_end": null,
"cdna_length": 6122,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145371.2"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.1149C>T",
"hgvs_p": "p.Ile383Ile",
"transcript": "NM_001145372.2",
"protein_id": "NP_001138844.1",
"transcript_support_level": null,
"aa_start": 383,
"aa_end": null,
"aa_length": 581,
"cds_start": 1149,
"cds_end": null,
"cds_length": 1746,
"cdna_start": 1534,
"cdna_end": null,
"cdna_length": 5987,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145372.2"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2208C>T",
"hgvs_p": "p.Ile736Ile",
"transcript": "XM_011518888.3",
"protein_id": "XP_011517190.1",
"transcript_support_level": null,
"aa_start": 736,
"aa_end": null,
"aa_length": 934,
"cds_start": 2208,
"cds_end": null,
"cds_length": 2805,
"cdna_start": 2352,
"cdna_end": null,
"cdna_length": 6805,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011518888.3"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2190C>T",
"hgvs_p": "p.Ile730Ile",
"transcript": "XM_047423635.1",
"protein_id": "XP_047279591.1",
"transcript_support_level": null,
"aa_start": 730,
"aa_end": null,
"aa_length": 928,
"cds_start": 2190,
"cds_end": null,
"cds_length": 2787,
"cdna_start": 2294,
"cdna_end": null,
"cdna_length": 6747,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047423635.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2178C>T",
"hgvs_p": "p.Ile726Ile",
"transcript": "XM_047423636.1",
"protein_id": "XP_047279592.1",
"transcript_support_level": null,
"aa_start": 726,
"aa_end": null,
"aa_length": 924,
"cds_start": 2178,
"cds_end": null,
"cds_length": 2775,
"cdna_start": 6187,
"cdna_end": null,
"cdna_length": 10640,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047423636.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.2145C>T",
"hgvs_p": "p.Ile715Ile",
"transcript": "XM_006717199.4",
"protein_id": "XP_006717262.1",
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"aa_start": 715,
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],
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"splice_prediction_selected": "Benign",
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"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
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"acmg_classification": "Benign",
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"acmg_by_gene": [
{
"score": -15,
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"criteria": [
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"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_002829.4",
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"effects": [
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],
"inheritance_mode": "Unknown",
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],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}