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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: 12-57471538-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=57471538&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 57471538,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000228682.7",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI1",
"gene_hgnc_id": 4317,
"hgvs_c": "c.2798G>A",
"hgvs_p": "p.Gly933Asp",
"transcript": "NM_005269.3",
"protein_id": "NP_005260.1",
"transcript_support_level": null,
"aa_start": 933,
"aa_end": null,
"aa_length": 1106,
"cds_start": 2798,
"cds_end": null,
"cds_length": 3321,
"cdna_start": 3242,
"cdna_end": null,
"cdna_length": 3972,
"mane_select": "ENST00000228682.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI1",
"gene_hgnc_id": 4317,
"hgvs_c": "c.2798G>A",
"hgvs_p": "p.Gly933Asp",
"transcript": "ENST00000228682.7",
"protein_id": "ENSP00000228682.2",
"transcript_support_level": 1,
"aa_start": 933,
"aa_end": null,
"aa_length": 1106,
"cds_start": 2798,
"cds_end": null,
"cds_length": 3321,
"cdna_start": 3242,
"cdna_end": null,
"cdna_length": 3972,
"mane_select": "NM_005269.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI1",
"gene_hgnc_id": 4317,
"hgvs_c": "c.2675G>A",
"hgvs_p": "p.Gly892Asp",
"transcript": "ENST00000528467.1",
"protein_id": "ENSP00000434408.1",
"transcript_support_level": 1,
"aa_start": 892,
"aa_end": null,
"aa_length": 1064,
"cds_start": 2675,
"cds_end": null,
"cds_length": 3196,
"cdna_start": 2675,
"cdna_end": null,
"cdna_length": 3196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI1",
"gene_hgnc_id": 4317,
"hgvs_c": "c.2675G>A",
"hgvs_p": "p.Gly892Asp",
"transcript": "NM_001167609.2",
"protein_id": "NP_001161081.1",
"transcript_support_level": null,
"aa_start": 892,
"aa_end": null,
"aa_length": 1065,
"cds_start": 2675,
"cds_end": null,
"cds_length": 3198,
"cdna_start": 3119,
"cdna_end": null,
"cdna_length": 3849,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI1",
"gene_hgnc_id": 4317,
"hgvs_c": "c.2675G>A",
"hgvs_p": "p.Gly892Asp",
"transcript": "ENST00000546141.5",
"protein_id": "ENSP00000441006.1",
"transcript_support_level": 5,
"aa_start": 892,
"aa_end": null,
"aa_length": 1065,
"cds_start": 2675,
"cds_end": null,
"cds_length": 3198,
"cdna_start": 2753,
"cdna_end": null,
"cdna_length": 3475,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI1",
"gene_hgnc_id": 4317,
"hgvs_c": "c.2414G>A",
"hgvs_p": "p.Gly805Asp",
"transcript": "NM_001160045.2",
"protein_id": "NP_001153517.1",
"transcript_support_level": null,
"aa_start": 805,
"aa_end": null,
"aa_length": 978,
"cds_start": 2414,
"cds_end": null,
"cds_length": 2937,
"cdna_start": 3022,
"cdna_end": null,
"cdna_length": 3752,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI1",
"gene_hgnc_id": 4317,
"hgvs_c": "c.2414G>A",
"hgvs_p": "p.Gly805Asp",
"transcript": "ENST00000543426.5",
"protein_id": "ENSP00000437607.1",
"transcript_support_level": 5,
"aa_start": 805,
"aa_end": null,
"aa_length": 978,
"cds_start": 2414,
"cds_end": null,
"cds_length": 2937,
"cdna_start": 2672,
"cdna_end": null,
"cdna_length": 3394,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI1",
"gene_hgnc_id": 4317,
"hgvs_c": "c.2798G>A",
"hgvs_p": "p.Gly933Asp",
"transcript": "XM_011538189.3",
"protein_id": "XP_011536491.1",
"transcript_support_level": null,
"aa_start": 933,
"aa_end": null,
"aa_length": 1106,
"cds_start": 2798,
"cds_end": null,
"cds_length": 3321,
"cdna_start": 3104,
"cdna_end": null,
"cdna_length": 3834,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLI1",
"gene_hgnc_id": 4317,
"hgvs_c": "c.2567G>A",
"hgvs_p": "p.Gly856Asp",
"transcript": "XM_011538190.3",
"protein_id": "XP_011536492.1",
"transcript_support_level": null,
"aa_start": 856,
"aa_end": null,
"aa_length": 1029,
"cds_start": 2567,
"cds_end": null,
"cds_length": 3090,
"cdna_start": 3011,
"cdna_end": null,
"cdna_length": 3741,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GLI1",
"gene_hgnc_id": 4317,
"dbsnp": "rs2228224",
"frequency_reference_population": 0.5761383,
"hom_count_reference_population": 278661,
"allele_count_reference_population": 928690,
"gnomad_exomes_af": 0.586481,
"gnomad_genomes_af": 0.476703,
"gnomad_exomes_ac": 856294,
"gnomad_genomes_ac": 72396,
"gnomad_exomes_homalt": 259186,
"gnomad_genomes_homalt": 19475,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.00006134262366686016,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.06,
"revel_prediction": "Benign",
"alphamissense_score": 0.1023,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.925,
"phylop100way_prediction": "Benign",
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000228682.7",
"gene_symbol": "GLI1",
"hgnc_id": 4317,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD,Unknown",
"hgvs_c": "c.2798G>A",
"hgvs_p": "p.Gly933Asp"
}
],
"clinvar_disease": " postaxial, type A8,GLI1-related disorder,Polydactyly,Polydactyly of a biphalangeal thumb,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "Polydactyly, postaxial, type A8|not provided|Polydactyly of a biphalangeal thumb|GLI1-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}