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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: X-153726084-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=153726084&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 153726084,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001440747.1",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "c.818C>A",
"hgvs_p": "p.Ala273Glu",
"transcript": "NM_000033.4",
"protein_id": "NP_000024.2",
"transcript_support_level": null,
"aa_start": 273,
"aa_end": null,
"aa_length": 745,
"cds_start": 818,
"cds_end": null,
"cds_length": 2238,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000218104.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000033.4"
},
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "c.818C>A",
"hgvs_p": "p.Ala273Glu",
"transcript": "ENST00000218104.6",
"protein_id": "ENSP00000218104.3",
"transcript_support_level": 1,
"aa_start": 273,
"aa_end": null,
"aa_length": 745,
"cds_start": 818,
"cds_end": null,
"cds_length": 2238,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000033.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000218104.6"
},
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "c.818C>A",
"hgvs_p": "p.Ala273Glu",
"transcript": "NM_001440747.1",
"protein_id": "NP_001427676.1",
"transcript_support_level": null,
"aa_start": 273,
"aa_end": null,
"aa_length": 845,
"cds_start": 818,
"cds_end": null,
"cds_length": 2538,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440747.1"
},
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "c.818C>A",
"hgvs_p": "p.Ala273Glu",
"transcript": "ENST00000862307.1",
"protein_id": "ENSP00000532366.1",
"transcript_support_level": null,
"aa_start": 273,
"aa_end": null,
"aa_length": 845,
"cds_start": 818,
"cds_end": null,
"cds_length": 2538,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862307.1"
},
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "c.818C>A",
"hgvs_p": "p.Ala273Glu",
"transcript": "ENST00000862306.1",
"protein_id": "ENSP00000532365.1",
"transcript_support_level": null,
"aa_start": 273,
"aa_end": null,
"aa_length": 835,
"cds_start": 818,
"cds_end": null,
"cds_length": 2508,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862306.1"
},
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "c.818C>A",
"hgvs_p": "p.Ala273Glu",
"transcript": "ENST00000935199.1",
"protein_id": "ENSP00000605258.1",
"transcript_support_level": null,
"aa_start": 273,
"aa_end": null,
"aa_length": 776,
"cds_start": 818,
"cds_end": null,
"cds_length": 2331,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000935199.1"
},
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "c.818C>A",
"hgvs_p": "p.Ala273Glu",
"transcript": "ENST00000968902.1",
"protein_id": "ENSP00000638961.1",
"transcript_support_level": null,
"aa_start": 273,
"aa_end": null,
"aa_length": 743,
"cds_start": 818,
"cds_end": null,
"cds_length": 2232,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000968902.1"
},
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "c.263C>A",
"hgvs_p": "p.Ala88Glu",
"transcript": "ENST00000370129.4",
"protein_id": "ENSP00000359147.3",
"transcript_support_level": 2,
"aa_start": 88,
"aa_end": null,
"aa_length": 227,
"cds_start": 263,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370129.4"
},
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "c.818C>A",
"hgvs_p": "p.Ala273Glu",
"transcript": "XM_047441917.1",
"protein_id": "XP_047297873.1",
"transcript_support_level": null,
"aa_start": 273,
"aa_end": null,
"aa_length": 575,
"cds_start": 818,
"cds_end": null,
"cds_length": 1728,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047441917.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCAP31",
"gene_hgnc_id": 16695,
"hgvs_c": "c.-403G>T",
"hgvs_p": null,
"transcript": "ENST00000862067.1",
"protein_id": "ENSP00000532126.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 246,
"cds_start": null,
"cds_end": null,
"cds_length": 741,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862067.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCAP31",
"gene_hgnc_id": 16695,
"hgvs_c": "c.-403G>T",
"hgvs_p": null,
"transcript": "ENST00000968754.1",
"protein_id": "ENSP00000638813.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 244,
"cds_start": null,
"cds_end": null,
"cds_length": 735,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000968754.1"
}
],
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"dbsnp": "rs868992338",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9138282537460327,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.87,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8213,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.78,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.557,
"phylop100way_prediction": "Pathogenic",
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM1",
"PM2",
"PP3_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_001440747.1",
"gene_symbol": "ABCD1",
"hgnc_id": 61,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL,AD",
"hgvs_c": "c.818C>A",
"hgvs_p": "p.Ala273Glu"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000862067.1",
"gene_symbol": "BCAP31",
"hgnc_id": 16695,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "XL,AR",
"hgvs_c": "c.-403G>T",
"hgvs_p": null
}
],
"clinvar_disease": "Adrenoleukodystrophy",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Adrenoleukodystrophy",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}