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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: 9-92718565-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=92718565&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 92718565,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000356884.11",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BICD2",
"gene_hgnc_id": 17208,
"hgvs_c": "c.2080C>A",
"hgvs_p": "p.Arg694Ser",
"transcript": "NM_001003800.2",
"protein_id": "NP_001003800.1",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 855,
"cds_start": 2080,
"cds_end": null,
"cds_length": 2568,
"cdna_start": 2169,
"cdna_end": null,
"cdna_length": 6448,
"mane_select": "ENST00000356884.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BICD2",
"gene_hgnc_id": 17208,
"hgvs_c": "c.2080C>A",
"hgvs_p": "p.Arg694Ser",
"transcript": "ENST00000356884.11",
"protein_id": "ENSP00000349351.6",
"transcript_support_level": 1,
"aa_start": 694,
"aa_end": null,
"aa_length": 855,
"cds_start": 2080,
"cds_end": null,
"cds_length": 2568,
"cdna_start": 2169,
"cdna_end": null,
"cdna_length": 6448,
"mane_select": "NM_001003800.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BICD2",
"gene_hgnc_id": 17208,
"hgvs_c": "c.2080C>A",
"hgvs_p": "p.Arg694Ser",
"transcript": "ENST00000375512.3",
"protein_id": "ENSP00000364662.3",
"transcript_support_level": 1,
"aa_start": 694,
"aa_end": null,
"aa_length": 824,
"cds_start": 2080,
"cds_end": null,
"cds_length": 2475,
"cdna_start": 2148,
"cdna_end": null,
"cdna_length": 4636,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BICD2",
"gene_hgnc_id": 17208,
"hgvs_c": "c.2080C>A",
"hgvs_p": "p.Arg694Ser",
"transcript": "NM_015250.4",
"protein_id": "NP_056065.1",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 824,
"cds_start": 2080,
"cds_end": null,
"cds_length": 2475,
"cdna_start": 2169,
"cdna_end": null,
"cdna_length": 4657,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BICD2",
"gene_hgnc_id": 17208,
"hgvs_c": "c.2161C>A",
"hgvs_p": "p.Arg721Ser",
"transcript": "XM_017014551.2",
"protein_id": "XP_016870040.1",
"transcript_support_level": null,
"aa_start": 721,
"aa_end": null,
"aa_length": 851,
"cds_start": 2161,
"cds_end": null,
"cds_length": 2556,
"cdna_start": 2250,
"cdna_end": null,
"cdna_length": 4738,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "BICD2",
"gene_hgnc_id": 17208,
"dbsnp": "rs797045412",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9179720878601074,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.596,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9996,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.27,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.159,
"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": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Moderate",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000356884.11",
"gene_symbol": "BICD2",
"hgnc_id": 17208,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2080C>A",
"hgvs_p": "p.Arg694Ser"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}