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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: 16-50723365-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=50723365&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "NOD2",
"hgnc_id": 5331,
"hgvs_c": "c.2863G>T",
"hgvs_p": "p.Val955Phe",
"inheritance_mode": "Unknown,AD",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_022162.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.1155,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.45,
"chr": "16",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.12583744525909424,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 1013,
"aa_ref": "V",
"aa_start": 928,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4363,
"cdna_start": 2847,
"cds_end": null,
"cds_length": 3042,
"cds_start": 2782,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001370466.1",
"gene_hgnc_id": 5331,
"gene_symbol": "NOD2",
"hgvs_c": "c.2782G>T",
"hgvs_p": "p.Val928Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000647318.2",
"protein_coding": true,
"protein_id": "NP_001357395.1",
"strand": true,
"transcript": "NM_001370466.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 1013,
"aa_ref": "V",
"aa_start": 928,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4363,
"cdna_start": 2847,
"cds_end": null,
"cds_length": 3042,
"cds_start": 2782,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000647318.2",
"gene_hgnc_id": 5331,
"gene_symbol": "NOD2",
"hgvs_c": "c.2782G>T",
"hgvs_p": "p.Val928Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001370466.1",
"protein_coding": true,
"protein_id": "ENSP00000495993.1",
"strand": true,
"transcript": "ENST00000647318.2",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 1040,
"aa_ref": "V",
"aa_start": 955,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4486,
"cdna_start": 2968,
"cds_end": null,
"cds_length": 3123,
"cds_start": 2863,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000300589.6",
"gene_hgnc_id": 5331,
"gene_symbol": "NOD2",
"hgvs_c": "c.2863G>T",
"hgvs_p": "p.Val955Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000300589.2",
"strand": true,
"transcript": "ENST00000300589.6",
"transcript_support_level": 1
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 167,
"aa_ref": "V",
"aa_start": 166,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 506,
"cdna_start": 497,
"cds_end": null,
"cds_length": 505,
"cds_start": 496,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000534057.1",
"gene_hgnc_id": 5331,
"gene_symbol": "NOD2",
"hgvs_c": "c.496G>T",
"hgvs_p": "p.Val166Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000437246.1",
"strand": true,
"transcript": "ENST00000534057.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 366,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000524712.5",
"gene_hgnc_id": 5331,
"gene_symbol": "NOD2",
"hgvs_c": "n.*176G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000464065.1",
"strand": true,
"transcript": "ENST00000524712.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 338,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000527052.5",
"gene_hgnc_id": 5331,
"gene_symbol": "NOD2",
"hgvs_c": "n.*148G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000463423.1",
"strand": true,
"transcript": "ENST00000527052.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 450,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000529633.5",
"gene_hgnc_id": 5331,
"gene_symbol": "NOD2",
"hgvs_c": "n.*260G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000462443.1",
"strand": true,
"transcript": "ENST00000529633.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 602,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000534067.5",
"gene_hgnc_id": 5331,
"gene_symbol": "NOD2",
"hgvs_c": "n.*412G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000463145.1",
"strand": true,
"transcript": "ENST00000534067.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 366,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000524712.5",
"gene_hgnc_id": 5331,
"gene_symbol": "NOD2",
"hgvs_c": "n.*176G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000464065.1",
"strand": true,
"transcript": "ENST00000524712.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 338,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000527052.5",
"gene_hgnc_id": 5331,
"gene_symbol": "NOD2",
"hgvs_c": "n.*148G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000463423.1",
"strand": true,
"transcript": "ENST00000527052.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 450,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000529633.5",
"gene_hgnc_id": 5331,
"gene_symbol": "NOD2",
"hgvs_c": "n.*260G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000462443.1",
"strand": true,
"transcript": "ENST00000529633.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 602,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000534067.5",
"gene_hgnc_id": 5331,
"gene_symbol": "NOD2",
"hgvs_c": "n.*412G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000463145.1",
"strand": true,
"transcript": "ENST00000534067.5",
"transcript_support_level": 1
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 1040,
"aa_ref": "V",
"aa_start": 955,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4675,
"cdna_start": 3159,
"cds_end": null,
"cds_length": 3123,
"cds_start": 2863,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_022162.3",
"gene_hgnc_id": 5331,
"gene_symbol": "NOD2",
"hgvs_c": "c.2863G>T",
"hgvs_p": "p.Val955Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_071445.1",
"strand": true,
"transcript": "NM_022162.3",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 1013,
"aa_ref": "V",
"aa_start": 928,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4414,
"cdna_start": 2898,
"cds_end": null,
"cds_length": 3042,
"cds_start": 2782,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001293557.2",
"gene_hgnc_id": 5331,
"gene_symbol": "NOD2",
"hgvs_c": "c.2782G>T",
"hgvs_p": "p.Val928Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001280486.1",
"strand": true,
"transcript": "NM_001293557.2",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 1013,
"aa_ref": "V",
"aa_start": 928,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4801,
"cdna_start": 3012,
"cds_end": null,
"cds_length": 3042,
"cds_start": 2782,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000951248.1",
"gene_hgnc_id": 5331,
"gene_symbol": "NOD2",
"hgvs_c": "c.2782G>T",
"hgvs_p": "p.Val928Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621307.1",
"strand": true,
"transcript": "ENST00000951248.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 167,
"aa_ref": "V",
"aa_start": 166,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 506,
"cdna_start": 497,
"cds_end": null,
"cds_length": 505,
"cds_start": 496,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000697426.1",
"gene_hgnc_id": 5331,
"gene_symbol": "NOD2",
"hgvs_c": "c.496G>T",
"hgvs_p": "p.Val166Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000513311.1",
"strand": true,
"transcript": "ENST00000697426.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 985,
"aa_ref": "V",
"aa_start": 900,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4279,
"cdna_start": 2763,
"cds_end": null,
"cds_length": 2958,
"cds_start": 2698,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_006721242.5",
"gene_hgnc_id": 5331,
"gene_symbol": "NOD2",
"hgvs_c": "c.2698G>T",
"hgvs_p": "p.Val900Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006721305.1",
"strand": true,
"transcript": "XM_006721242.5",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 872,
"aa_ref": "V",
"aa_start": 787,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4379,
"cdna_start": 2863,
"cds_end": null,
"cds_length": 2619,
"cds_start": 2359,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_047434452.1",
"gene_hgnc_id": 5331,
"gene_symbol": "NOD2",
"hgvs_c": "c.2359G>T",
"hgvs_p": "p.Val787Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047290408.1",
"strand": true,
"transcript": "XM_047434452.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 872,
"aa_ref": "V",
"aa_start": 787,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3969,
"cdna_start": 2453,
"cds_end": null,
"cds_length": 2619,
"cds_start": 2359,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_047434453.1",
"gene_hgnc_id": 5331,
"gene_symbol": "NOD2",
"hgvs_c": "c.2359G>T",
"hgvs_p": "p.Val787Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047290409.1",
"strand": true,
"transcript": "XM_047434453.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 872,
"aa_ref": "V",
"aa_start": 787,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4020,
"cdna_start": 2504,
"cds_end": null,
"cds_length": 2619,
"cds_start": 2359,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_047434454.1",
"gene_hgnc_id": 5331,
"gene_symbol": "NOD2",
"hgvs_c": "c.2359G>T",
"hgvs_p": "p.Val787Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047290410.1",
"strand": true,
"transcript": "XM_047434454.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 818,
"aa_ref": "V",
"aa_start": 733,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3896,
"cdna_start": 2380,
"cds_end": null,
"cds_length": 2457,
"cds_start": 2197,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_017023536.2",
"gene_hgnc_id": 5331,
"gene_symbol": "NOD2",
"hgvs_c": "c.2197G>T",
"hgvs_p": "p.Val733Phe",
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