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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: 4-55965784-TC-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=55965784&ref=TC&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 55965784,
"ref": "TC",
"alt": "T",
"effect": "frameshift_variant",
"transcript": "ENST00000257287.5",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "c.970delC",
"hgvs_p": "p.Gln324fs",
"transcript": "NM_025009.5",
"protein_id": "NP_079285.2",
"transcript_support_level": null,
"aa_start": 324,
"aa_end": null,
"aa_length": 1140,
"cds_start": 970,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 1130,
"cdna_end": null,
"cdna_length": 5596,
"mane_select": "ENST00000257287.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "c.970delC",
"hgvs_p": "p.Gln324fs",
"transcript": "ENST00000257287.5",
"protein_id": "ENSP00000257287.3",
"transcript_support_level": 1,
"aa_start": 324,
"aa_end": null,
"aa_length": 1140,
"cds_start": 970,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 1130,
"cdna_end": null,
"cdna_length": 5596,
"mane_select": "NM_025009.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "n.920delC",
"hgvs_p": null,
"transcript": "ENST00000506202.1",
"protein_id": null,
"transcript_support_level": 1,
"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": 5129,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "c.970delC",
"hgvs_p": "p.Gln324fs",
"transcript": "XM_006714055.4",
"protein_id": "XP_006714118.1",
"transcript_support_level": null,
"aa_start": 324,
"aa_end": null,
"aa_length": 1129,
"cds_start": 970,
"cds_end": null,
"cds_length": 3390,
"cdna_start": 1130,
"cdna_end": null,
"cdna_length": 5563,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "n.604delC",
"hgvs_p": null,
"transcript": "ENST00000515081.1",
"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": 1399,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "c.-98delC",
"hgvs_p": null,
"transcript": "XM_005265788.5",
"protein_id": "XP_005265845.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 783,
"cds_start": -4,
"cds_end": null,
"cds_length": 2352,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4476,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LOC124900705",
"gene_hgnc_id": null,
"hgvs_c": "n.197+4988delG",
"hgvs_p": null,
"transcript": "XR_007058124.1",
"protein_id": null,
"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": 278,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LOC124900705",
"gene_hgnc_id": null,
"hgvs_c": "n.286-782delG",
"hgvs_p": null,
"transcript": "XR_007058125.1",
"protein_id": null,
"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": 394,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"dbsnp": "rs202247811",
"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": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 5.046,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.03,
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "ENST00000257287.5",
"gene_symbol": "CEP135",
"hgnc_id": 29086,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.970delC",
"hgvs_p": "p.Gln324fs"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "XR_007058124.1",
"gene_symbol": "LOC124900705",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.197+4988delG",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal recessive, primary,Microcephaly 8",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Microcephaly 8, primary, autosomal recessive",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}