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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: 5-173235071-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=173235071&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 173235071,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000329198.5",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKX2-5",
"gene_hgnc_id": 2488,
"hgvs_c": "c.13C>T",
"hgvs_p": "p.Pro5Ser",
"transcript": "NM_004387.4",
"protein_id": "NP_004378.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 324,
"cds_start": 13,
"cds_end": null,
"cds_length": 975,
"cdna_start": 136,
"cdna_end": null,
"cdna_length": 1558,
"mane_select": "ENST00000329198.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKX2-5",
"gene_hgnc_id": 2488,
"hgvs_c": "c.13C>T",
"hgvs_p": "p.Pro5Ser",
"transcript": "ENST00000329198.5",
"protein_id": "ENSP00000327758.4",
"transcript_support_level": 1,
"aa_start": 5,
"aa_end": null,
"aa_length": 324,
"cds_start": 13,
"cds_end": null,
"cds_length": 975,
"cdna_start": 136,
"cdna_end": null,
"cdna_length": 1558,
"mane_select": "NM_004387.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKX2-5",
"gene_hgnc_id": 2488,
"hgvs_c": "c.13C>T",
"hgvs_p": "p.Pro5Ser",
"transcript": "ENST00000424406.2",
"protein_id": "ENSP00000395378.2",
"transcript_support_level": 1,
"aa_start": 5,
"aa_end": null,
"aa_length": 112,
"cds_start": 13,
"cds_end": null,
"cds_length": 339,
"cdna_start": 194,
"cdna_end": null,
"cdna_length": 1124,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKX2-5",
"gene_hgnc_id": 2488,
"hgvs_c": "c.13C>T",
"hgvs_p": "p.Pro5Ser",
"transcript": "NM_001166176.2",
"protein_id": "NP_001159648.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 151,
"cds_start": 13,
"cds_end": null,
"cds_length": 456,
"cdna_start": 136,
"cdna_end": null,
"cdna_length": 1813,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKX2-5",
"gene_hgnc_id": 2488,
"hgvs_c": "c.13C>T",
"hgvs_p": "p.Pro5Ser",
"transcript": "ENST00000521848.1",
"protein_id": "ENSP00000427906.1",
"transcript_support_level": 2,
"aa_start": 5,
"aa_end": null,
"aa_length": 151,
"cds_start": 13,
"cds_end": null,
"cds_length": 456,
"cdna_start": 136,
"cdna_end": null,
"cdna_length": 1027,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKX2-5",
"gene_hgnc_id": 2488,
"hgvs_c": "c.13C>T",
"hgvs_p": "p.Pro5Ser",
"transcript": "ENST00000517440.1",
"protein_id": "ENSP00000429905.1",
"transcript_support_level": 4,
"aa_start": 5,
"aa_end": null,
"aa_length": 141,
"cds_start": 13,
"cds_end": null,
"cds_length": 427,
"cdna_start": 241,
"cdna_end": null,
"cdna_length": 655,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKX2-5",
"gene_hgnc_id": 2488,
"hgvs_c": "c.13C>T",
"hgvs_p": "p.Pro5Ser",
"transcript": "NM_001166175.2",
"protein_id": "NP_001159647.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 112,
"cds_start": 13,
"cds_end": null,
"cds_length": 339,
"cdna_start": 136,
"cdna_end": null,
"cdna_length": 1850,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKX2-5",
"gene_hgnc_id": 2488,
"hgvs_c": "c.13C>T",
"hgvs_p": "p.Pro5Ser",
"transcript": "XM_017009071.3",
"protein_id": "XP_016864560.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 142,
"cds_start": 13,
"cds_end": null,
"cds_length": 429,
"cdna_start": 136,
"cdna_end": null,
"cdna_length": 1089,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NKX2-5",
"gene_hgnc_id": 2488,
"dbsnp": "rs769233111",
"frequency_reference_population": 0.000013690481,
"hom_count_reference_population": 0,
"allele_count_reference_population": 22,
"gnomad_exomes_af": 0.0000130603,
"gnomad_genomes_af": 0.0000197148,
"gnomad_exomes_ac": 19,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4567406177520752,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.538,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.088,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.09,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.076,
"phylop100way_prediction": "Uncertain_significance",
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS1_Supporting,BS2",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BS1_Supporting",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000329198.5",
"gene_symbol": "NKX2-5",
"hgnc_id": 2488,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown,SD",
"hgvs_c": "c.13C>T",
"hgvs_p": "p.Pro5Ser"
}
],
"clinvar_disease": "6 conditions,Atrial septal defect 7,Cardiovascular phenotype,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:4",
"phenotype_combined": "Atrial septal defect 7|not specified|6 conditions|Cardiovascular phenotype",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}