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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: 19-47021156-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=47021156&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 47021156,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_002517.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS1",
"gene_hgnc_id": 7894,
"hgvs_c": "c.109C>G",
"hgvs_p": "p.Pro37Ala",
"transcript": "NM_002517.4",
"protein_id": "NP_002508.2",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 590,
"cds_start": 109,
"cds_end": null,
"cds_length": 1773,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000602212.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002517.4"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS1",
"gene_hgnc_id": 7894,
"hgvs_c": "c.109C>G",
"hgvs_p": "p.Pro37Ala",
"transcript": "ENST00000602212.6",
"protein_id": "ENSP00000469142.1",
"transcript_support_level": 1,
"aa_start": 37,
"aa_end": null,
"aa_length": 590,
"cds_start": 109,
"cds_end": null,
"cds_length": 1773,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002517.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000602212.6"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS1",
"gene_hgnc_id": 7894,
"hgvs_c": "c.109C>G",
"hgvs_p": "p.Pro37Ala",
"transcript": "ENST00000449844.6",
"protein_id": "ENSP00000405290.1",
"transcript_support_level": 1,
"aa_start": 37,
"aa_end": null,
"aa_length": 590,
"cds_start": 109,
"cds_end": null,
"cds_length": 1773,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000449844.6"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS1",
"gene_hgnc_id": 7894,
"hgvs_c": "c.109C>G",
"hgvs_p": "p.Pro37Ala",
"transcript": "ENST00000906441.1",
"protein_id": "ENSP00000576500.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 650,
"cds_start": 109,
"cds_end": null,
"cds_length": 1953,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906441.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS1",
"gene_hgnc_id": 7894,
"hgvs_c": "c.109C>G",
"hgvs_p": "p.Pro37Ala",
"transcript": "ENST00000906440.1",
"protein_id": "ENSP00000576499.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 590,
"cds_start": 109,
"cds_end": null,
"cds_length": 1773,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906440.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS1",
"gene_hgnc_id": 7894,
"hgvs_c": "c.109C>G",
"hgvs_p": "p.Pro37Ala",
"transcript": "ENST00000941427.1",
"protein_id": "ENSP00000611486.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 590,
"cds_start": 109,
"cds_end": null,
"cds_length": 1773,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000941427.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS1",
"gene_hgnc_id": 7894,
"hgvs_c": "c.109C>G",
"hgvs_p": "p.Pro37Ala",
"transcript": "ENST00000941428.1",
"protein_id": "ENSP00000611487.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 590,
"cds_start": 109,
"cds_end": null,
"cds_length": 1773,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000941428.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"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": "NPAS1",
"gene_hgnc_id": 7894,
"hgvs_c": "c.109C>G",
"hgvs_p": "p.Pro37Ala",
"transcript": "ENST00000940003.1",
"protein_id": "ENSP00000610062.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 506,
"cds_start": 109,
"cds_end": null,
"cds_length": 1521,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940003.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS1",
"gene_hgnc_id": 7894,
"hgvs_c": "c.109C>G",
"hgvs_p": "p.Pro37Ala",
"transcript": "XM_047438881.1",
"protein_id": "XP_047294837.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 650,
"cds_start": 109,
"cds_end": null,
"cds_length": 1953,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047438881.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS1",
"gene_hgnc_id": 7894,
"hgvs_c": "c.109C>G",
"hgvs_p": "p.Pro37Ala",
"transcript": "XM_047438882.1",
"protein_id": "XP_047294838.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 591,
"cds_start": 109,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047438882.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS1",
"gene_hgnc_id": 7894,
"hgvs_c": "c.109C>G",
"hgvs_p": "p.Pro37Ala",
"transcript": "XM_047438883.1",
"protein_id": "XP_047294839.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 521,
"cds_start": 109,
"cds_end": null,
"cds_length": 1566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047438883.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"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": "NPAS1",
"gene_hgnc_id": 7894,
"hgvs_c": "c.109C>G",
"hgvs_p": "p.Pro37Ala",
"transcript": "XM_024451526.2",
"protein_id": "XP_024307294.2",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 483,
"cds_start": 109,
"cds_end": null,
"cds_length": 1452,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024451526.2"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS1",
"gene_hgnc_id": 7894,
"hgvs_c": "c.109C>G",
"hgvs_p": "p.Pro37Ala",
"transcript": "XM_047438885.1",
"protein_id": "XP_047294841.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 454,
"cds_start": 109,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047438885.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS1",
"gene_hgnc_id": 7894,
"hgvs_c": "c.109C>G",
"hgvs_p": "p.Pro37Ala",
"transcript": "XM_047438886.1",
"protein_id": "XP_047294842.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 453,
"cds_start": 109,
"cds_end": null,
"cds_length": 1362,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047438886.1"
},
{
"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": 1,
"intron_rank_end": null,
"gene_symbol": "NPAS1",
"gene_hgnc_id": 7894,
"hgvs_c": "c.-171+1159C>G",
"hgvs_p": null,
"transcript": "ENST00000602189.5",
"protein_id": "ENSP00000472679.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 415,
"cds_start": null,
"cds_end": null,
"cds_length": 1248,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000602189.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000307953",
"gene_hgnc_id": null,
"hgvs_c": "n.190+146G>C",
"hgvs_p": null,
"transcript": "ENST00000830040.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000830040.1"
}
],
"gene_symbol": "NPAS1",
"gene_hgnc_id": 7894,
"dbsnp": "rs753078765",
"frequency_reference_population": 0.00009318796,
"hom_count_reference_population": 0,
"allele_count_reference_population": 148,
"gnomad_exomes_af": 0.0000877065,
"gnomad_genomes_af": 0.00014514,
"gnomad_exomes_ac": 126,
"gnomad_genomes_ac": 22,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.009855985641479492,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.123,
"revel_prediction": "Benign",
"alphamissense_score": 0.059,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.221,
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_002517.4",
"gene_symbol": "NPAS1",
"hgnc_id": 7894,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.109C>G",
"hgvs_p": "p.Pro37Ala"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000830040.1",
"gene_symbol": "ENSG00000307953",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.190+146G>C",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}