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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-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=92718565&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 92718565,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000356884.11",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"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>T",
"hgvs_p": "p.Arg694Cys",
"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": "C",
"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>T",
"hgvs_p": "p.Arg694Cys",
"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": "C",
"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>T",
"hgvs_p": "p.Arg694Cys",
"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": "C",
"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>T",
"hgvs_p": "p.Arg694Cys",
"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": "C",
"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>T",
"hgvs_p": "p.Arg721Cys",
"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": 0.9401484727859497,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.772,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9944,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.28,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000356884.11",
"gene_symbol": "BICD2",
"hgnc_id": 17208,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2080C>T",
"hgvs_p": "p.Arg694Cys"
}
],
"clinvar_disease": " 2, 2b, AD, autosomal dominant, lower extremity-predominant, prenatal onset,Autosomal dominant childhood-onset proximal spinal muscular atrophy with contractures,Autosomal dominant hereditary axonal motor and sensory neuropathy,Spinal muscular atrophy,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:3",
"phenotype_combined": "Spinal muscular atrophy, lower extremity-predominant, 2, AD|Autosomal dominant childhood-onset proximal spinal muscular atrophy with contractures|Spinal muscular atrophy, lower extremity-predominant, 2b, prenatal onset, autosomal dominant|not provided|Autosomal dominant hereditary axonal motor and sensory neuropathy",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}