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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: 21-44292992-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=44292992&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1_Strong",
"PS3",
"PM2",
"PP5_Very_Strong"
],
"effects": [
"splice_acceptor_variant",
"intron_variant"
],
"gene_symbol": "AIRE",
"hgnc_id": 360,
"hgvs_c": "c.1096-1G>A",
"hgvs_p": null,
"inheritance_mode": "AR,AD",
"pathogenic_score": 18,
"score": 18,
"transcript": "NM_000383.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1_Strong,PS3,PM2,PP5_Very_Strong",
"acmg_score": 18,
"allele_count_reference_population": 2,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.27,
"chr": "21",
"clinvar_classification": "Pathogenic",
"clinvar_disease": " type 1,Polyglandular autoimmune syndrome",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.27000001072883606,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 545,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2690,
"cdna_start": null,
"cds_end": null,
"cds_length": 1638,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_000383.4",
"gene_hgnc_id": 360,
"gene_symbol": "AIRE",
"hgvs_c": "c.1096-1G>A",
"hgvs_p": null,
"intron_rank": 9,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000291582.6",
"protein_coding": true,
"protein_id": "NP_000374.1",
"strand": true,
"transcript": "NM_000383.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 545,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2690,
"cdna_start": null,
"cds_end": null,
"cds_length": 1638,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000291582.6",
"gene_hgnc_id": 360,
"gene_symbol": "AIRE",
"hgvs_c": "c.1096-1G>A",
"hgvs_p": null,
"intron_rank": 9,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000383.4",
"protein_coding": true,
"protein_id": "ENSP00000291582.5",
"strand": true,
"transcript": "ENST00000291582.6",
"transcript_support_level": 1
},
{
"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": 1361,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000337909.5",
"gene_hgnc_id": 360,
"gene_symbol": "AIRE",
"hgvs_c": "n.557-1G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000337909.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 544,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2678,
"cdna_start": null,
"cds_end": null,
"cds_length": 1635,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000966178.1",
"gene_hgnc_id": 360,
"gene_symbol": "AIRE",
"hgvs_c": "c.1093-1G>A",
"hgvs_p": null,
"intron_rank": 9,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000636237.1",
"strand": true,
"transcript": "ENST00000966178.1",
"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": 1279,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000397994.8",
"gene_hgnc_id": 360,
"gene_symbol": "AIRE",
"hgvs_c": "n.557-1G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000397994.8",
"transcript_support_level": 5
},
{
"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": 2409,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000527919.5",
"gene_hgnc_id": 360,
"gene_symbol": "AIRE",
"hgvs_c": "n.1826-1G>A",
"hgvs_p": null,
"intron_rank": 9,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000527919.5",
"transcript_support_level": 2
},
{
"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": 4306,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 12,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000530812.5",
"gene_hgnc_id": 360,
"gene_symbol": "AIRE",
"hgvs_c": "n.2843-1G>A",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000530812.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999939108429288,
"dbsnp": "rs780906602",
"effect": "splice_acceptor_variant,intron_variant",
"frequency_reference_population": 0.0000012405932,
"gene_hgnc_id": 360,
"gene_symbol": "AIRE",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84955e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000657108,
"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": "Pathogenic",
"phenotype_combined": "Polyglandular autoimmune syndrome, type 1",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.937,
"pos": 44292992,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.7639999985694885,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Pathogenic",
"spliceai_max_score": 0.89,
"transcript": "NM_000383.4"
}
]
}