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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: 7-129209348-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=129209348&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 129209348,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000249373.8",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMO",
"gene_hgnc_id": 11119,
"hgvs_c": "c.1417G>A",
"hgvs_p": "p.Asp473Asn",
"transcript": "NM_005631.5",
"protein_id": "NP_005622.1",
"transcript_support_level": null,
"aa_start": 473,
"aa_end": null,
"aa_length": 787,
"cds_start": 1417,
"cds_end": null,
"cds_length": 2364,
"cdna_start": 1936,
"cdna_end": null,
"cdna_length": 3977,
"mane_select": "ENST00000249373.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMO",
"gene_hgnc_id": 11119,
"hgvs_c": "c.1417G>A",
"hgvs_p": "p.Asp473Asn",
"transcript": "ENST00000249373.8",
"protein_id": "ENSP00000249373.3",
"transcript_support_level": 1,
"aa_start": 473,
"aa_end": null,
"aa_length": 787,
"cds_start": 1417,
"cds_end": null,
"cds_length": 2364,
"cdna_start": 1936,
"cdna_end": null,
"cdna_length": 3977,
"mane_select": "NM_005631.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMO",
"gene_hgnc_id": 11119,
"hgvs_c": "c.1027G>A",
"hgvs_p": "p.Asp343Asn",
"transcript": "XM_047420759.1",
"protein_id": "XP_047276715.1",
"transcript_support_level": null,
"aa_start": 343,
"aa_end": null,
"aa_length": 657,
"cds_start": 1027,
"cds_end": null,
"cds_length": 1974,
"cdna_start": 2050,
"cdna_end": null,
"cdna_length": 4091,
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SMO",
"gene_hgnc_id": 11119,
"hgvs_c": "n.436+497G>A",
"hgvs_p": null,
"transcript": "ENST00000462420.2",
"protein_id": "ENSP00000418720.2",
"transcript_support_level": 4,
"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": 787,
"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": 12,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SMO",
"gene_hgnc_id": 11119,
"hgvs_c": "n.*1221+497G>A",
"hgvs_p": null,
"transcript": "ENST00000655644.1",
"protein_id": "ENSP00000499377.1",
"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": 3997,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMO",
"gene_hgnc_id": 11119,
"hgvs_c": "n.*67G>A",
"hgvs_p": null,
"transcript": "ENST00000495998.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 732,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SMO",
"gene_hgnc_id": 11119,
"dbsnp": "rs17710891",
"frequency_reference_population": 0.000016109745,
"hom_count_reference_population": 0,
"allele_count_reference_population": 26,
"gnomad_exomes_af": 0.0000171023,
"gnomad_genomes_af": 0.00000657307,
"gnomad_exomes_ac": 25,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.871209979057312,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.682,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8716,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.15,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.876,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.01,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate,BS1_Supporting",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate",
"BS1_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000249373.8",
"gene_symbol": "SMO",
"hgnc_id": 11119,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1417G>A",
"hgvs_p": "p.Asp473Asn"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "not provided",
"clinvar_review_status": "no classification provided",
"clinvar_submissions_summary": "O:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "not provided",
"custom_annotations": null
}
],
"message": null
}