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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: 2-232480203-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=232480203&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 232480203,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000304546.6",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ECEL1",
"gene_hgnc_id": 3147,
"hgvs_c": "c.2278T>C",
"hgvs_p": "p.Cys760Arg",
"transcript": "NM_004826.4",
"protein_id": "NP_004817.2",
"transcript_support_level": null,
"aa_start": 760,
"aa_end": null,
"aa_length": 775,
"cds_start": 2278,
"cds_end": null,
"cds_length": 2328,
"cdna_start": 2495,
"cdna_end": null,
"cdna_length": 2871,
"mane_select": "ENST00000304546.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ECEL1",
"gene_hgnc_id": 3147,
"hgvs_c": "c.2278T>C",
"hgvs_p": "p.Cys760Arg",
"transcript": "ENST00000304546.6",
"protein_id": "ENSP00000302051.1",
"transcript_support_level": 1,
"aa_start": 760,
"aa_end": null,
"aa_length": 775,
"cds_start": 2278,
"cds_end": null,
"cds_length": 2328,
"cdna_start": 2495,
"cdna_end": null,
"cdna_length": 2871,
"mane_select": "NM_004826.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ECEL1",
"gene_hgnc_id": 3147,
"hgvs_c": "c.2272T>C",
"hgvs_p": "p.Cys758Arg",
"transcript": "ENST00000409941.1",
"protein_id": "ENSP00000386333.1",
"transcript_support_level": 1,
"aa_start": 758,
"aa_end": null,
"aa_length": 773,
"cds_start": 2272,
"cds_end": null,
"cds_length": 2322,
"cdna_start": 2272,
"cdna_end": null,
"cdna_length": 2322,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ECEL1",
"gene_hgnc_id": 3147,
"hgvs_c": "c.2272T>C",
"hgvs_p": "p.Cys758Arg",
"transcript": "NM_001290787.2",
"protein_id": "NP_001277716.1",
"transcript_support_level": null,
"aa_start": 758,
"aa_end": null,
"aa_length": 773,
"cds_start": 2272,
"cds_end": null,
"cds_length": 2322,
"cdna_start": 2489,
"cdna_end": null,
"cdna_length": 2865,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ECEL1",
"gene_hgnc_id": 3147,
"hgvs_c": "c.457T>C",
"hgvs_p": "p.Cys153Arg",
"transcript": "ENST00000411860.5",
"protein_id": "ENSP00000412683.1",
"transcript_support_level": 3,
"aa_start": 153,
"aa_end": null,
"aa_length": 168,
"cds_start": 457,
"cds_end": null,
"cds_length": 507,
"cdna_start": 457,
"cdna_end": null,
"cdna_length": 833,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ECEL1",
"gene_hgnc_id": 3147,
"hgvs_c": "n.2589T>C",
"hgvs_p": null,
"transcript": "ENST00000482346.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 2965,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ECEL1",
"gene_hgnc_id": 3147,
"dbsnp": "rs587777129",
"frequency_reference_population": 0.0000065783415,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.00000657834,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9896026849746704,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.948,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9961,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.48,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.75,
"phylop100way_prediction": "Pathogenic",
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000304546.6",
"gene_symbol": "ECEL1",
"hgnc_id": 3147,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2278T>C",
"hgvs_p": "p.Cys760Arg"
}
],
"clinvar_disease": "Distal arthrogryposis type 5D",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Distal arthrogryposis type 5D",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}