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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: 4-86769845-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=86769845&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 86769845,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_080685.3",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.4566A>G",
"hgvs_p": "p.Ile1522Met",
"transcript": "NM_080683.3",
"protein_id": "NP_542414.1",
"transcript_support_level": null,
"aa_start": 1522,
"aa_end": null,
"aa_length": 2485,
"cds_start": 4566,
"cds_end": null,
"cds_length": 7458,
"cdna_start": 5046,
"cdna_end": null,
"cdna_length": 8548,
"mane_select": "ENST00000411767.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_080683.3"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.4566A>G",
"hgvs_p": "p.Ile1522Met",
"transcript": "ENST00000411767.7",
"protein_id": "ENSP00000407249.2",
"transcript_support_level": 1,
"aa_start": 1522,
"aa_end": null,
"aa_length": 2485,
"cds_start": 4566,
"cds_end": null,
"cds_length": 7458,
"cdna_start": 5046,
"cdna_end": null,
"cdna_length": 8548,
"mane_select": "NM_080683.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000411767.7"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.4509A>G",
"hgvs_p": "p.Ile1503Met",
"transcript": "ENST00000427191.6",
"protein_id": "ENSP00000408368.2",
"transcript_support_level": 1,
"aa_start": 1503,
"aa_end": null,
"aa_length": 2466,
"cds_start": 4509,
"cds_end": null,
"cds_length": 7401,
"cdna_start": 4989,
"cdna_end": null,
"cdna_length": 8487,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000427191.6"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.3993A>G",
"hgvs_p": "p.Ile1331Met",
"transcript": "ENST00000316707.10",
"protein_id": "ENSP00000322675.6",
"transcript_support_level": 1,
"aa_start": 1331,
"aa_end": null,
"aa_length": 2294,
"cds_start": 3993,
"cds_end": null,
"cds_length": 6885,
"cdna_start": 4056,
"cdna_end": null,
"cdna_length": 7546,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000316707.10"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.4566A>G",
"hgvs_p": "p.Ile1522Met",
"transcript": "ENST00000940454.1",
"protein_id": "ENSP00000610513.1",
"transcript_support_level": null,
"aa_start": 1522,
"aa_end": null,
"aa_length": 2502,
"cds_start": 4566,
"cds_end": null,
"cds_length": 7509,
"cdna_start": 5040,
"cdna_end": null,
"cdna_length": 8588,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940454.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.4581A>G",
"hgvs_p": "p.Ile1527Met",
"transcript": "NM_080685.3",
"protein_id": "NP_542416.1",
"transcript_support_level": null,
"aa_start": 1527,
"aa_end": null,
"aa_length": 2490,
"cds_start": 4581,
"cds_end": null,
"cds_length": 7473,
"cdna_start": 5061,
"cdna_end": null,
"cdna_length": 8563,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_080685.3"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.4581A>G",
"hgvs_p": "p.Ile1527Met",
"transcript": "ENST00000436978.5",
"protein_id": "ENSP00000394794.1",
"transcript_support_level": 5,
"aa_start": 1527,
"aa_end": null,
"aa_length": 2490,
"cds_start": 4581,
"cds_end": null,
"cds_length": 7473,
"cdna_start": 5061,
"cdna_end": null,
"cdna_length": 8573,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000436978.5"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.4581A>G",
"hgvs_p": "p.Ile1527Met",
"transcript": "ENST00000511467.1",
"protein_id": "ENSP00000426626.1",
"transcript_support_level": 2,
"aa_start": 1527,
"aa_end": null,
"aa_length": 2490,
"cds_start": 4581,
"cds_end": null,
"cds_length": 7473,
"cdna_start": 4586,
"cdna_end": null,
"cdna_length": 8076,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000511467.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.4524A>G",
"hgvs_p": "p.Ile1508Met",
"transcript": "ENST00000940452.1",
"protein_id": "ENSP00000610511.1",
"transcript_support_level": null,
"aa_start": 1508,
"aa_end": null,
"aa_length": 2488,
"cds_start": 4524,
"cds_end": null,
"cds_length": 7467,
"cdna_start": 5003,
"cdna_end": null,
"cdna_length": 8567,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940452.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.4509A>G",
"hgvs_p": "p.Ile1503Met",
"transcript": "ENST00000860771.1",
"protein_id": "ENSP00000530830.1",
"transcript_support_level": null,
"aa_start": 1503,
"aa_end": null,
"aa_length": 2483,
"cds_start": 4509,
"cds_end": null,
"cds_length": 7452,
"cdna_start": 4979,
"cdna_end": null,
"cdna_length": 8550,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000860771.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.4524A>G",
"hgvs_p": "p.Ile1508Met",
"transcript": "ENST00000940451.1",
"protein_id": "ENSP00000610510.1",
"transcript_support_level": null,
"aa_start": 1508,
"aa_end": null,
"aa_length": 2471,
"cds_start": 4524,
"cds_end": null,
"cds_length": 7416,
"cdna_start": 5043,
"cdna_end": null,
"cdna_length": 8564,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940451.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.4521A>G",
"hgvs_p": "p.Ile1507Met",
"transcript": "ENST00000940456.1",
"protein_id": "ENSP00000610515.1",
"transcript_support_level": null,
"aa_start": 1507,
"aa_end": null,
"aa_length": 2470,
"cds_start": 4521,
"cds_end": null,
"cds_length": 7413,
"cdna_start": 4995,
"cdna_end": null,
"cdna_length": 8487,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940456.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.4509A>G",
"hgvs_p": "p.Ile1503Met",
"transcript": "NM_006264.3",
"protein_id": "NP_006255.1",
"transcript_support_level": null,
"aa_start": 1503,
"aa_end": null,
"aa_length": 2466,
"cds_start": 4509,
"cds_end": null,
"cds_length": 7401,
"cdna_start": 4989,
"cdna_end": null,
"cdna_length": 8491,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006264.3"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.4488A>G",
"hgvs_p": "p.Ile1496Met",
"transcript": "ENST00000940457.1",
"protein_id": "ENSP00000610516.1",
"transcript_support_level": null,
"aa_start": 1496,
"aa_end": null,
"aa_length": 2459,
"cds_start": 4488,
"cds_end": null,
"cds_length": 7380,
"cdna_start": 4949,
"cdna_end": null,
"cdna_length": 8451,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940457.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.4314A>G",
"hgvs_p": "p.Ile1438Met",
"transcript": "ENST00000940459.1",
"protein_id": "ENSP00000610518.1",
"transcript_support_level": null,
"aa_start": 1438,
"aa_end": null,
"aa_length": 2401,
"cds_start": 4314,
"cds_end": null,
"cds_length": 7206,
"cdna_start": 4760,
"cdna_end": null,
"cdna_length": 8250,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940459.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.4020A>G",
"hgvs_p": "p.Ile1340Met",
"transcript": "ENST00000940458.1",
"protein_id": "ENSP00000610517.1",
"transcript_support_level": null,
"aa_start": 1340,
"aa_end": null,
"aa_length": 2320,
"cds_start": 4020,
"cds_end": null,
"cds_length": 6963,
"cdna_start": 4466,
"cdna_end": null,
"cdna_length": 8009,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940458.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.4005A>G",
"hgvs_p": "p.Ile1335Met",
"transcript": "ENST00000953522.1",
"protein_id": "ENSP00000623581.1",
"transcript_support_level": null,
"aa_start": 1335,
"aa_end": null,
"aa_length": 2315,
"cds_start": 4005,
"cds_end": null,
"cds_length": 6948,
"cdna_start": 4479,
"cdna_end": null,
"cdna_length": 8020,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953522.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.4050A>G",
"hgvs_p": "p.Ile1350Met",
"transcript": "ENST00000940455.1",
"protein_id": "ENSP00000610514.1",
"transcript_support_level": null,
"aa_start": 1350,
"aa_end": null,
"aa_length": 2313,
"cds_start": 4050,
"cds_end": null,
"cds_length": 6942,
"cdna_start": 4529,
"cdna_end": null,
"cdna_length": 8018,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940455.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.4008A>G",
"hgvs_p": "p.Ile1336Met",
"transcript": "ENST00000860769.1",
"protein_id": "ENSP00000530828.1",
"transcript_support_level": null,
"aa_start": 1336,
"aa_end": null,
"aa_length": 2299,
"cds_start": 4008,
"cds_end": null,
"cds_length": 6900,
"cdna_start": 4859,
"cdna_end": null,
"cdna_length": 8379,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000860769.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.4005A>G",
"hgvs_p": "p.Ile1335Met",
"transcript": "ENST00000860770.1",
"protein_id": "ENSP00000530829.1",
"transcript_support_level": null,
"aa_start": 1335,
"aa_end": null,
"aa_length": 2298,
"cds_start": 4005,
"cds_end": null,
"cds_length": 6897,
"cdna_start": 4485,
"cdna_end": null,
"cdna_length": 8002,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000860770.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.3993A>G",
"hgvs_p": "p.Ile1331Met",
"transcript": "NM_080684.3",
"protein_id": "NP_542415.1",
"transcript_support_level": null,
"aa_start": 1331,
"aa_end": null,
"aa_length": 2294,
"cds_start": 3993,
"cds_end": null,
"cds_length": 6885,
"cdna_start": 4473,
"cdna_end": null,
"cdna_length": 7975,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_080684.3"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN13",
"gene_hgnc_id": 9646,
"hgvs_c": "c.3948A>G",
"hgvs_p": "p.Ile1316Met",
"transcript": "ENST00000860772.1",
"protein_id": "ENSP00000530831.1",
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"hom_count_reference_population": 26340,
"allele_count_reference_population": 277844,
"gnomad_exomes_af": 0.175111,
"gnomad_genomes_af": 0.144661,
"gnomad_exomes_ac": 255831,
"gnomad_genomes_ac": 22013,
"gnomad_exomes_homalt": 24336,
"gnomad_genomes_homalt": 2004,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0040934085845947266,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.025,
"revel_prediction": "Benign",
"alphamissense_score": 0.0985,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.63,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.142,
"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.4581A>G",
"hgvs_p": "p.Ile1527Met"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}