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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: 16-50712288-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=50712288&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 50712288,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001370466.1",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2296G>A",
"hgvs_p": "p.Val766Met",
"transcript": "NM_001370466.1",
"protein_id": "NP_001357395.1",
"transcript_support_level": null,
"aa_start": 766,
"aa_end": null,
"aa_length": 1013,
"cds_start": 2296,
"cds_end": null,
"cds_length": 3042,
"cdna_start": 2361,
"cdna_end": null,
"cdna_length": 4363,
"mane_select": "ENST00000647318.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2296G>A",
"hgvs_p": "p.Val766Met",
"transcript": "ENST00000647318.2",
"protein_id": "ENSP00000495993.1",
"transcript_support_level": null,
"aa_start": 766,
"aa_end": null,
"aa_length": 1013,
"cds_start": 2296,
"cds_end": null,
"cds_length": 3042,
"cdna_start": 2361,
"cdna_end": null,
"cdna_length": 4363,
"mane_select": "NM_001370466.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2377G>A",
"hgvs_p": "p.Val793Met",
"transcript": "ENST00000300589.6",
"protein_id": "ENSP00000300589.2",
"transcript_support_level": 1,
"aa_start": 793,
"aa_end": null,
"aa_length": 1040,
"cds_start": 2377,
"cds_end": null,
"cds_length": 3123,
"cdna_start": 2482,
"cdna_end": null,
"cdna_length": 4486,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.94G>A",
"hgvs_p": "p.Val32Met",
"transcript": "ENST00000534057.1",
"protein_id": "ENSP00000437246.1",
"transcript_support_level": 1,
"aa_start": 32,
"aa_end": null,
"aa_length": 167,
"cds_start": 94,
"cds_end": null,
"cds_length": 505,
"cdna_start": 95,
"cdna_end": null,
"cdna_length": 506,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "n.94G>A",
"hgvs_p": null,
"transcript": "ENST00000524712.5",
"protein_id": "ENSP00000464065.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 366,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "n.94G>A",
"hgvs_p": null,
"transcript": "ENST00000527052.5",
"protein_id": "ENSP00000463423.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 338,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "n.94G>A",
"hgvs_p": null,
"transcript": "ENST00000529633.5",
"protein_id": "ENSP00000462443.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 450,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "n.94G>A",
"hgvs_p": null,
"transcript": "ENST00000534067.5",
"protein_id": "ENSP00000463145.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 602,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2377G>A",
"hgvs_p": "p.Val793Met",
"transcript": "NM_022162.3",
"protein_id": "NP_071445.1",
"transcript_support_level": null,
"aa_start": 793,
"aa_end": null,
"aa_length": 1040,
"cds_start": 2377,
"cds_end": null,
"cds_length": 3123,
"cdna_start": 2673,
"cdna_end": null,
"cdna_length": 4675,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2296G>A",
"hgvs_p": "p.Val766Met",
"transcript": "NM_001293557.2",
"protein_id": "NP_001280486.1",
"transcript_support_level": null,
"aa_start": 766,
"aa_end": null,
"aa_length": 1013,
"cds_start": 2296,
"cds_end": null,
"cds_length": 3042,
"cdna_start": 2412,
"cdna_end": null,
"cdna_length": 4414,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.94G>A",
"hgvs_p": "p.Val32Met",
"transcript": "ENST00000697426.1",
"protein_id": "ENSP00000513311.1",
"transcript_support_level": null,
"aa_start": 32,
"aa_end": null,
"aa_length": 167,
"cds_start": 94,
"cds_end": null,
"cds_length": 505,
"cdna_start": 95,
"cdna_end": null,
"cdna_length": 506,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2296G>A",
"hgvs_p": "p.Val766Met",
"transcript": "XM_006721242.5",
"protein_id": "XP_006721305.1",
"transcript_support_level": null,
"aa_start": 766,
"aa_end": null,
"aa_length": 985,
"cds_start": 2296,
"cds_end": null,
"cds_length": 2958,
"cdna_start": 2361,
"cdna_end": null,
"cdna_length": 4279,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.1873G>A",
"hgvs_p": "p.Val625Met",
"transcript": "XM_047434452.1",
"protein_id": "XP_047290408.1",
"transcript_support_level": null,
"aa_start": 625,
"aa_end": null,
"aa_length": 872,
"cds_start": 1873,
"cds_end": null,
"cds_length": 2619,
"cdna_start": 2377,
"cdna_end": null,
"cdna_length": 4379,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.1873G>A",
"hgvs_p": "p.Val625Met",
"transcript": "XM_047434453.1",
"protein_id": "XP_047290409.1",
"transcript_support_level": null,
"aa_start": 625,
"aa_end": null,
"aa_length": 872,
"cds_start": 1873,
"cds_end": null,
"cds_length": 2619,
"cdna_start": 1967,
"cdna_end": null,
"cdna_length": 3969,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.1873G>A",
"hgvs_p": "p.Val625Met",
"transcript": "XM_047434454.1",
"protein_id": "XP_047290410.1",
"transcript_support_level": null,
"aa_start": 625,
"aa_end": null,
"aa_length": 872,
"cds_start": 1873,
"cds_end": null,
"cds_length": 2619,
"cdna_start": 2018,
"cdna_end": null,
"cdna_length": 4020,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.1711G>A",
"hgvs_p": "p.Val571Met",
"transcript": "XM_017023536.2",
"protein_id": "XP_016879025.1",
"transcript_support_level": null,
"aa_start": 571,
"aa_end": null,
"aa_length": 818,
"cds_start": 1711,
"cds_end": null,
"cds_length": 2457,
"cdna_start": 1894,
"cdna_end": null,
"cdna_length": 3896,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.1711G>A",
"hgvs_p": "p.Val571Met",
"transcript": "XM_017023537.2",
"protein_id": "XP_016879026.1",
"transcript_support_level": null,
"aa_start": 571,
"aa_end": null,
"aa_length": 818,
"cds_start": 1711,
"cds_end": null,
"cds_length": 2457,
"cdna_start": 1788,
"cdna_end": null,
"cdna_length": 3790,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2296G>A",
"hgvs_p": "p.Val766Met",
"transcript": "XM_006721243.5",
"protein_id": "XP_006721306.1",
"transcript_support_level": null,
"aa_start": 766,
"aa_end": null,
"aa_length": 793,
"cds_start": 2296,
"cds_end": null,
"cds_length": 2382,
"cdna_start": 2361,
"cdna_end": null,
"cdna_length": 2920,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2296G>A",
"hgvs_p": "p.Val766Met",
"transcript": "XM_011523260.4",
"protein_id": "XP_011521562.1",
"transcript_support_level": null,
"aa_start": 766,
"aa_end": null,
"aa_length": 793,
"cds_start": 2296,
"cds_end": null,
"cds_length": 2382,
"cdna_start": 2361,
"cdna_end": null,
"cdna_length": 2948,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2296G>A",
"hgvs_p": "p.Val766Met",
"transcript": "XM_011523261.3",
"protein_id": "XP_011521563.1",
"transcript_support_level": null,
"aa_start": 766,
"aa_end": null,
"aa_length": 793,
"cds_start": 2296,
"cds_end": null,
"cds_length": 2382,
"cdna_start": 2361,
"cdna_end": null,
"cdna_length": 3283,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2296G>A",
"hgvs_p": "p.Val766Met",
"transcript": "XM_047434455.1",
"protein_id": "XP_047290411.1",
"transcript_support_level": null,
"aa_start": 766,
"aa_end": null,
"aa_length": 793,
"cds_start": 2296,
"cds_end": null,
"cds_length": 2382,
"cdna_start": 2361,
"cdna_end": null,
"cdna_length": 2542,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2296G>A",
"hgvs_p": "p.Val766Met",
"transcript": "XM_047434456.1",
"protein_id": "XP_047290412.1",
"transcript_support_level": null,
"aa_start": 766,
"aa_end": null,
"aa_length": 793,
"cds_start": 2296,
"cds_end": null,
"cds_length": 2382,
"cdna_start": 2361,
"cdna_end": null,
"cdna_length": 2530,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2296G>A",
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}
],
"gene_symbol": "NOD2",
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"dbsnp": "rs104895444",
"frequency_reference_population": 0.0015285158,
"hom_count_reference_population": 9,
"allele_count_reference_population": 2467,
"gnomad_exomes_af": 0.00156335,
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"gnomad_genomes_ac": 182,
"gnomad_exomes_homalt": 9,
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"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.025483131408691406,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.289,
"revel_prediction": "Benign",
"alphamissense_score": 0.1669,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.28,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.031,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001370466.1",
"gene_symbol": "NOD2",
"hgnc_id": 5331,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.2296G>A",
"hgvs_p": "p.Val766Met"
}
],
"clinvar_disease": "Autoinflammatory syndrome,Blau syndrome,Inflammatory bowel disease 1,NOD2-related disorder,Regional enteritis,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:5 B:1 O:1",
"phenotype_combined": "Blau syndrome|not provided|Autoinflammatory syndrome|Inflammatory bowel disease 1|Regional enteritis;Blau syndrome|NOD2-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}