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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: 4-86785353-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=86785353&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 86785353,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_080685.3",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.6241T>G",
"hgvs_p": "p.Tyr2081Asp",
"transcript": "NM_080683.3",
"protein_id": "NP_542414.1",
"transcript_support_level": null,
"aa_start": 2081,
"aa_end": null,
"aa_length": 2485,
"cds_start": 6241,
"cds_end": null,
"cds_length": 7458,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000411767.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_080683.3"
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.6241T>G",
"hgvs_p": "p.Tyr2081Asp",
"transcript": "ENST00000411767.7",
"protein_id": "ENSP00000407249.2",
"transcript_support_level": 1,
"aa_start": 2081,
"aa_end": null,
"aa_length": 2485,
"cds_start": 6241,
"cds_end": null,
"cds_length": 7458,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_080683.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000411767.7"
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.6184T>G",
"hgvs_p": "p.Tyr2062Asp",
"transcript": "ENST00000427191.6",
"protein_id": "ENSP00000408368.2",
"transcript_support_level": 1,
"aa_start": 2062,
"aa_end": null,
"aa_length": 2466,
"cds_start": 6184,
"cds_end": null,
"cds_length": 7401,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000427191.6"
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.5668T>G",
"hgvs_p": "p.Tyr1890Asp",
"transcript": "ENST00000316707.10",
"protein_id": "ENSP00000322675.6",
"transcript_support_level": 1,
"aa_start": 1890,
"aa_end": null,
"aa_length": 2294,
"cds_start": 5668,
"cds_end": null,
"cds_length": 6885,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000316707.10"
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.6292T>G",
"hgvs_p": "p.Tyr2098Asp",
"transcript": "ENST00000940454.1",
"protein_id": "ENSP00000610513.1",
"transcript_support_level": null,
"aa_start": 2098,
"aa_end": null,
"aa_length": 2502,
"cds_start": 6292,
"cds_end": null,
"cds_length": 7509,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940454.1"
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.6256T>G",
"hgvs_p": "p.Tyr2086Asp",
"transcript": "NM_080685.3",
"protein_id": "NP_542416.1",
"transcript_support_level": null,
"aa_start": 2086,
"aa_end": null,
"aa_length": 2490,
"cds_start": 6256,
"cds_end": null,
"cds_length": 7473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_080685.3"
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.6256T>G",
"hgvs_p": "p.Tyr2086Asp",
"transcript": "ENST00000436978.5",
"protein_id": "ENSP00000394794.1",
"transcript_support_level": 5,
"aa_start": 2086,
"aa_end": null,
"aa_length": 2490,
"cds_start": 6256,
"cds_end": null,
"cds_length": 7473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000436978.5"
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.6256T>G",
"hgvs_p": "p.Tyr2086Asp",
"transcript": "ENST00000511467.1",
"protein_id": "ENSP00000426626.1",
"transcript_support_level": 2,
"aa_start": 2086,
"aa_end": null,
"aa_length": 2490,
"cds_start": 6256,
"cds_end": null,
"cds_length": 7473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000511467.1"
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.6250T>G",
"hgvs_p": "p.Tyr2084Asp",
"transcript": "ENST00000940452.1",
"protein_id": "ENSP00000610511.1",
"transcript_support_level": null,
"aa_start": 2084,
"aa_end": null,
"aa_length": 2488,
"cds_start": 6250,
"cds_end": null,
"cds_length": 7467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940452.1"
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.6235T>G",
"hgvs_p": "p.Tyr2079Asp",
"transcript": "ENST00000860771.1",
"protein_id": "ENSP00000530830.1",
"transcript_support_level": null,
"aa_start": 2079,
"aa_end": null,
"aa_length": 2483,
"cds_start": 6235,
"cds_end": null,
"cds_length": 7452,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000860771.1"
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.6199T>G",
"hgvs_p": "p.Tyr2067Asp",
"transcript": "ENST00000940451.1",
"protein_id": "ENSP00000610510.1",
"transcript_support_level": null,
"aa_start": 2067,
"aa_end": null,
"aa_length": 2471,
"cds_start": 6199,
"cds_end": null,
"cds_length": 7416,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940451.1"
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.6196T>G",
"hgvs_p": "p.Tyr2066Asp",
"transcript": "ENST00000940456.1",
"protein_id": "ENSP00000610515.1",
"transcript_support_level": null,
"aa_start": 2066,
"aa_end": null,
"aa_length": 2470,
"cds_start": 6196,
"cds_end": null,
"cds_length": 7413,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940456.1"
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.6184T>G",
"hgvs_p": "p.Tyr2062Asp",
"transcript": "NM_006264.3",
"protein_id": "NP_006255.1",
"transcript_support_level": null,
"aa_start": 2062,
"aa_end": null,
"aa_length": 2466,
"cds_start": 6184,
"cds_end": null,
"cds_length": 7401,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006264.3"
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.6163T>G",
"hgvs_p": "p.Tyr2055Asp",
"transcript": "ENST00000940457.1",
"protein_id": "ENSP00000610516.1",
"transcript_support_level": null,
"aa_start": 2055,
"aa_end": null,
"aa_length": 2459,
"cds_start": 6163,
"cds_end": null,
"cds_length": 7380,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940457.1"
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.5989T>G",
"hgvs_p": "p.Tyr1997Asp",
"transcript": "ENST00000940459.1",
"protein_id": "ENSP00000610518.1",
"transcript_support_level": null,
"aa_start": 1997,
"aa_end": null,
"aa_length": 2401,
"cds_start": 5989,
"cds_end": null,
"cds_length": 7206,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940459.1"
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.5746T>G",
"hgvs_p": "p.Tyr1916Asp",
"transcript": "ENST00000940458.1",
"protein_id": "ENSP00000610517.1",
"transcript_support_level": null,
"aa_start": 1916,
"aa_end": null,
"aa_length": 2320,
"cds_start": 5746,
"cds_end": null,
"cds_length": 6963,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940458.1"
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.5731T>G",
"hgvs_p": "p.Tyr1911Asp",
"transcript": "ENST00000953522.1",
"protein_id": "ENSP00000623581.1",
"transcript_support_level": null,
"aa_start": 1911,
"aa_end": null,
"aa_length": 2315,
"cds_start": 5731,
"cds_end": null,
"cds_length": 6948,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953522.1"
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.5725T>G",
"hgvs_p": "p.Tyr1909Asp",
"transcript": "ENST00000940455.1",
"protein_id": "ENSP00000610514.1",
"transcript_support_level": null,
"aa_start": 1909,
"aa_end": null,
"aa_length": 2313,
"cds_start": 5725,
"cds_end": null,
"cds_length": 6942,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940455.1"
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.5683T>G",
"hgvs_p": "p.Tyr1895Asp",
"transcript": "ENST00000860769.1",
"protein_id": "ENSP00000530828.1",
"transcript_support_level": null,
"aa_start": 1895,
"aa_end": null,
"aa_length": 2299,
"cds_start": 5683,
"cds_end": null,
"cds_length": 6900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000860769.1"
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.5680T>G",
"hgvs_p": "p.Tyr1894Asp",
"transcript": "ENST00000860770.1",
"protein_id": "ENSP00000530829.1",
"transcript_support_level": null,
"aa_start": 1894,
"aa_end": null,
"aa_length": 2298,
"cds_start": 5680,
"cds_end": null,
"cds_length": 6897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000860770.1"
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.5668T>G",
"hgvs_p": "p.Tyr1890Asp",
"transcript": "NM_080684.3",
"protein_id": "NP_542415.1",
"transcript_support_level": null,
"aa_start": 1890,
"aa_end": null,
"aa_length": 2294,
"cds_start": 5668,
"cds_end": null,
"cds_length": 6885,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_080684.3"
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.5623T>G",
"hgvs_p": "p.Tyr1875Asp",
"transcript": "ENST00000860772.1",
"protein_id": "ENSP00000530831.1",
"transcript_support_level": null,
"aa_start": 1875,
"aa_end": null,
"aa_length": 2279,
"cds_start": 5623,
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"gnomad_genomes_homalt": 22507,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.00000194312201529101,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.06,
"revel_prediction": "Benign",
"alphamissense_score": 0.0454,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.75,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.399,
"phylop100way_prediction": "Benign",
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_080685.3",
"gene_symbol": "PTPN13",
"hgnc_id": 9646,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.6256T>G",
"hgvs_p": "p.Tyr2086Asp"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}