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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: 16-50724938-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=50724938&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 50724938,
"ref": "G",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000647318.2",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2802-551G>A",
"hgvs_p": null,
"transcript": "NM_001370466.1",
"protein_id": "NP_001357395.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1013,
"cds_start": -4,
"cds_end": null,
"cds_length": 3042,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4363,
"mane_select": "ENST00000647318.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2802-551G>A",
"hgvs_p": null,
"transcript": "ENST00000647318.2",
"protein_id": "ENSP00000495993.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1013,
"cds_start": -4,
"cds_end": null,
"cds_length": 3042,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4363,
"mane_select": "NM_001370466.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2883-551G>A",
"hgvs_p": null,
"transcript": "ENST00000300589.6",
"protein_id": "ENSP00000300589.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1040,
"cds_start": -4,
"cds_end": null,
"cds_length": 3123,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4486,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2883-551G>A",
"hgvs_p": null,
"transcript": "NM_022162.3",
"protein_id": "NP_071445.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1040,
"cds_start": -4,
"cds_end": null,
"cds_length": 3123,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4675,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2802-551G>A",
"hgvs_p": null,
"transcript": "NM_001293557.2",
"protein_id": "NP_001280486.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1013,
"cds_start": -4,
"cds_end": null,
"cds_length": 3042,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4414,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "n.2382-4880G>A",
"hgvs_p": null,
"transcript": "ENST00000641284.2",
"protein_id": "ENSP00000493088.1",
"transcript_support_level": null,
"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": 3830,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "n.*567-551G>A",
"hgvs_p": null,
"transcript": "ENST00000646677.2",
"protein_id": "ENSP00000496533.1",
"transcript_support_level": null,
"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": 4512,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "n.2280-551G>A",
"hgvs_p": null,
"transcript": "ENST00000697428.1",
"protein_id": null,
"transcript_support_level": null,
"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": 3774,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "n.3014-551G>A",
"hgvs_p": null,
"transcript": "NR_163434.1",
"protein_id": null,
"transcript_support_level": null,
"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": 4510,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2718-551G>A",
"hgvs_p": null,
"transcript": "XM_006721242.5",
"protein_id": "XP_006721305.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 985,
"cds_start": -4,
"cds_end": null,
"cds_length": 2958,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4279,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2379-551G>A",
"hgvs_p": null,
"transcript": "XM_047434452.1",
"protein_id": "XP_047290408.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 872,
"cds_start": -4,
"cds_end": null,
"cds_length": 2619,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4379,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2379-551G>A",
"hgvs_p": null,
"transcript": "XM_047434453.1",
"protein_id": "XP_047290409.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 872,
"cds_start": -4,
"cds_end": null,
"cds_length": 2619,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3969,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2379-551G>A",
"hgvs_p": null,
"transcript": "XM_047434454.1",
"protein_id": "XP_047290410.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 872,
"cds_start": -4,
"cds_end": null,
"cds_length": 2619,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4020,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2217-551G>A",
"hgvs_p": null,
"transcript": "XM_017023536.2",
"protein_id": "XP_016879025.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 818,
"cds_start": -4,
"cds_end": null,
"cds_length": 2457,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3896,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"hgvs_c": "c.2217-551G>A",
"hgvs_p": null,
"transcript": "XM_017023537.2",
"protein_id": "XP_016879026.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 818,
"cds_start": -4,
"cds_end": null,
"cds_length": 2457,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3790,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NOD2",
"gene_hgnc_id": 5331,
"dbsnp": "rs749910",
"frequency_reference_population": 0.16912161,
"hom_count_reference_population": 2868,
"allele_count_reference_population": 25742,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.169122,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 25742,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 2868,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7900000214576721,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.79,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.034,
"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": "ENST00000647318.2",
"gene_symbol": "NOD2",
"hgnc_id": 5331,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.2802-551G>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}