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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: 2-218890304-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=218890304&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 218890304,
"ref": "G",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000258411.8",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT10A",
"gene_hgnc_id": 13829,
"hgvs_c": "c.697G>T",
"hgvs_p": "p.Glu233*",
"transcript": "NM_025216.3",
"protein_id": "NP_079492.2",
"transcript_support_level": null,
"aa_start": 233,
"aa_end": null,
"aa_length": 417,
"cds_start": 697,
"cds_end": null,
"cds_length": 1254,
"cdna_start": 841,
"cdna_end": null,
"cdna_length": 2055,
"mane_select": "ENST00000258411.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT10A",
"gene_hgnc_id": 13829,
"hgvs_c": "c.697G>T",
"hgvs_p": "p.Glu233*",
"transcript": "ENST00000258411.8",
"protein_id": "ENSP00000258411.3",
"transcript_support_level": 1,
"aa_start": 233,
"aa_end": null,
"aa_length": 417,
"cds_start": 697,
"cds_end": null,
"cds_length": 1254,
"cdna_start": 841,
"cdna_end": null,
"cdna_length": 2055,
"mane_select": "NM_025216.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT10A",
"gene_hgnc_id": 13829,
"hgvs_c": "c.601G>T",
"hgvs_p": "p.Glu201*",
"transcript": "XM_011511929.3",
"protein_id": "XP_011510231.1",
"transcript_support_level": null,
"aa_start": 201,
"aa_end": null,
"aa_length": 385,
"cds_start": 601,
"cds_end": null,
"cds_length": 1158,
"cdna_start": 768,
"cdna_end": null,
"cdna_length": 1982,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "WNT10A",
"gene_hgnc_id": 13829,
"hgvs_c": "c.263-2470G>T",
"hgvs_p": null,
"transcript": "ENST00000458582.1",
"protein_id": "ENSP00000388812.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 210,
"cds_start": -4,
"cds_end": null,
"cds_length": 635,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 636,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "WNT10A",
"gene_hgnc_id": 13829,
"hgvs_c": "c.377-2470G>T",
"hgvs_p": null,
"transcript": "XM_011511930.2",
"protein_id": "XP_011510232.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 299,
"cds_start": -4,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1675,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT10A",
"gene_hgnc_id": 13829,
"hgvs_c": "n.*205G>T",
"hgvs_p": null,
"transcript": "ENST00000483911.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 590,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "WNT10A",
"gene_hgnc_id": 13829,
"dbsnp": "rs121908118",
"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": 0.6499999761581421,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.12999999523162842,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.65,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.813,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.13,
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000258411.8",
"gene_symbol": "WNT10A",
"hgnc_id": 13829,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR,SD,AD",
"hgvs_c": "c.697G>T",
"hgvs_p": "p.Glu233*"
}
],
"clinvar_disease": " 4, selective,Odonto-onycho-dermal dysplasia,Tooth agenesis",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Odonto-onycho-dermal dysplasia|Tooth agenesis, selective, 4;Odonto-onycho-dermal dysplasia",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}