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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: 16-88805738-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=88805738&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 8,
"criteria": [
"BP4_Strong",
"BS1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CDT1",
"hgnc_id": 24576,
"hgvs_c": "c.701G>C",
"hgvs_p": "p.Cys234Ser",
"inheritance_mode": "AR,AD",
"pathogenic_score": 0,
"score": -8,
"transcript": "NM_030928.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS1",
"acmg_score": -8,
"allele_count_reference_population": 35,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0972,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.72,
"chr": "16",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.012552648782730103,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 546,
"aa_ref": "C",
"aa_start": 234,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2664,
"cdna_start": 744,
"cds_end": null,
"cds_length": 1641,
"cds_start": 701,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_030928.4",
"gene_hgnc_id": 24576,
"gene_symbol": "CDT1",
"hgvs_c": "c.701G>C",
"hgvs_p": "p.Cys234Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000301019.9",
"protein_coding": true,
"protein_id": "NP_112190.2",
"strand": true,
"transcript": "NM_030928.4",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 546,
"aa_ref": "C",
"aa_start": 234,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2664,
"cdna_start": 744,
"cds_end": null,
"cds_length": 1641,
"cds_start": 701,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000301019.9",
"gene_hgnc_id": 24576,
"gene_symbol": "CDT1",
"hgvs_c": "c.701G>C",
"hgvs_p": "p.Cys234Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_030928.4",
"protein_coding": true,
"protein_id": "ENSP00000301019.4",
"strand": true,
"transcript": "ENST00000301019.9",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 553,
"aa_ref": "C",
"aa_start": 234,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1929,
"cdna_start": 740,
"cds_end": null,
"cds_length": 1662,
"cds_start": 701,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000929785.1",
"gene_hgnc_id": 24576,
"gene_symbol": "CDT1",
"hgvs_c": "c.701G>C",
"hgvs_p": "p.Cys234Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000599844.1",
"strand": true,
"transcript": "ENST00000929785.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 735,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000562747.1",
"gene_hgnc_id": 24576,
"gene_symbol": "CDT1",
"hgvs_c": "n.407G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000562747.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 188,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 571,
"cdna_start": null,
"cds_end": null,
"cds_length": 569,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000569140.1",
"gene_hgnc_id": 24576,
"gene_symbol": "CDT1",
"hgvs_c": "c.-32G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000456926.1",
"strand": true,
"transcript": "ENST00000569140.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs562796806",
"effect": "missense_variant",
"frequency_reference_population": 0.000021700662,
"gene_hgnc_id": 24576,
"gene_symbol": "CDT1",
"gnomad_exomes_ac": 31,
"gnomad_exomes_af": 0.0000212233,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 4,
"gnomad_genomes_af": 0.0000262816,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.646,
"pos": 88805738,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.062,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.05000000074505806,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.05,
"transcript": "NM_030928.4"
}
]
}