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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: 1-22129682-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=22129682&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 22129682,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000290167.11",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT4",
"gene_hgnc_id": 12783,
"hgvs_c": "c.247C>T",
"hgvs_p": "p.Arg83Trp",
"transcript": "NM_030761.5",
"protein_id": "NP_110388.2",
"transcript_support_level": null,
"aa_start": 83,
"aa_end": null,
"aa_length": 351,
"cds_start": 247,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 422,
"cdna_end": null,
"cdna_length": 3968,
"mane_select": "ENST00000290167.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT4",
"gene_hgnc_id": 12783,
"hgvs_c": "c.247C>T",
"hgvs_p": "p.Arg83Trp",
"transcript": "ENST00000290167.11",
"protein_id": "ENSP00000290167.5",
"transcript_support_level": 1,
"aa_start": 83,
"aa_end": null,
"aa_length": 351,
"cds_start": 247,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 422,
"cdna_end": null,
"cdna_length": 3968,
"mane_select": "NM_030761.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT4",
"gene_hgnc_id": 12783,
"hgvs_c": "c.169C>T",
"hgvs_p": "p.Arg57Trp",
"transcript": "ENST00000415567.1",
"protein_id": "ENSP00000403334.1",
"transcript_support_level": 2,
"aa_start": 57,
"aa_end": null,
"aa_length": 149,
"cds_start": 169,
"cds_end": null,
"cds_length": 450,
"cdna_start": 170,
"cdna_end": null,
"cdna_length": 680,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT4",
"gene_hgnc_id": 12783,
"hgvs_c": "c.82C>T",
"hgvs_p": "p.Arg28Trp",
"transcript": "ENST00000441048.1",
"protein_id": "ENSP00000388925.1",
"transcript_support_level": 5,
"aa_start": 28,
"aa_end": null,
"aa_length": 51,
"cds_start": 82,
"cds_end": null,
"cds_length": 156,
"cdna_start": 408,
"cdna_end": null,
"cdna_length": 482,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT4",
"gene_hgnc_id": 12783,
"hgvs_c": "c.313C>T",
"hgvs_p": "p.Arg105Trp",
"transcript": "XM_011541597.3",
"protein_id": "XP_011539899.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 373,
"cds_start": 313,
"cds_end": null,
"cds_length": 1122,
"cdna_start": 408,
"cdna_end": null,
"cdna_length": 3954,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WNT4",
"gene_hgnc_id": 12783,
"hgvs_c": "c.313C>T",
"hgvs_p": "p.Arg105Trp",
"transcript": "XM_011541599.2",
"protein_id": "XP_011539901.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 197,
"cds_start": 313,
"cds_end": null,
"cds_length": 594,
"cdna_start": 313,
"cdna_end": null,
"cdna_length": 828,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "WNT4",
"gene_hgnc_id": 12783,
"dbsnp": "rs121908652",
"frequency_reference_population": 0.000006816303,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000615762,
"gnomad_genomes_af": 0.0000131428,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9518357515335083,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.867,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.3438,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.35,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.54,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PP3_Strong",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000290167.11",
"gene_symbol": "WNT4",
"hgnc_id": 12783,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR,Unknown",
"hgvs_c": "c.247C>T",
"hgvs_p": "p.Arg83Trp"
}
],
"clinvar_disease": "Mullerian aplasia and hyperandrogenism",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Mullerian aplasia and hyperandrogenism",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}