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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: 22-45414328-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=45414328&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "RIBC2",
"hgnc_id": 13241,
"hgvs_c": "c.136A>T",
"hgvs_p": "p.Thr46Ser",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_015653.5",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_score": -4,
"allele_count_reference_population": 211,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.1129,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.76,
"chr": "22",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.006546288728713989,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 382,
"aa_ref": "T",
"aa_start": 46,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1490,
"cdna_start": 330,
"cds_end": null,
"cds_length": 1149,
"cds_start": 136,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_015653.5",
"gene_hgnc_id": 13241,
"gene_symbol": "RIBC2",
"hgvs_c": "c.136A>T",
"hgvs_p": "p.Thr46Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000614167.2",
"protein_coding": true,
"protein_id": "NP_056468.3",
"strand": true,
"transcript": "NM_015653.5",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 382,
"aa_ref": "T",
"aa_start": 46,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1490,
"cdna_start": 330,
"cds_end": null,
"cds_length": 1149,
"cds_start": 136,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000614167.2",
"gene_hgnc_id": 13241,
"gene_symbol": "RIBC2",
"hgvs_c": "c.136A>T",
"hgvs_p": "p.Thr46Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_015653.5",
"protein_coding": true,
"protein_id": "ENSP00000483356.1",
"strand": true,
"transcript": "ENST00000614167.2",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 193,
"aa_ref": "T",
"aa_start": 46,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1497,
"cdna_start": 330,
"cds_end": null,
"cds_length": 582,
"cds_start": 136,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_017028766.2",
"gene_hgnc_id": 13241,
"gene_symbol": "RIBC2",
"hgvs_c": "c.136A>T",
"hgvs_p": "p.Thr46Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016884255.1",
"strand": true,
"transcript": "XM_017028766.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 309,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1316,
"cdna_start": null,
"cds_end": null,
"cds_length": 930,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_005261524.5",
"gene_hgnc_id": 13241,
"gene_symbol": "RIBC2",
"hgvs_c": "c.-84A>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005261581.1",
"strand": true,
"transcript": "XM_005261524.5",
"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": 643,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000621287.1",
"gene_hgnc_id": 13241,
"gene_symbol": "RIBC2",
"hgvs_c": "n.6A>T",
"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": "ENST00000621287.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs140376917",
"effect": "missense_variant",
"frequency_reference_population": 0.00013609092,
"gene_hgnc_id": 13241,
"gene_symbol": "RIBC2",
"gnomad_exomes_ac": 102,
"gnomad_exomes_af": 0.0000729522,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 109,
"gnomad_genomes_af": 0.00071589,
"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": -0.036,
"pos": 45414328,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.032,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_015653.5"
}
]
}