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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: 12-6939151-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=6939151&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 6939151,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000396684.3",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATN1",
"gene_hgnc_id": 3033,
"hgvs_c": "c.3188T>G",
"hgvs_p": "p.Leu1063Arg",
"transcript": "NM_001940.4",
"protein_id": "NP_001931.2",
"transcript_support_level": null,
"aa_start": 1063,
"aa_end": null,
"aa_length": 1190,
"cds_start": 3188,
"cds_end": null,
"cds_length": 3573,
"cdna_start": 3776,
"cdna_end": null,
"cdna_length": 4702,
"mane_select": "ENST00000396684.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATN1",
"gene_hgnc_id": 3033,
"hgvs_c": "c.3188T>G",
"hgvs_p": "p.Leu1063Arg",
"transcript": "ENST00000396684.3",
"protein_id": "ENSP00000379915.2",
"transcript_support_level": 1,
"aa_start": 1063,
"aa_end": null,
"aa_length": 1190,
"cds_start": 3188,
"cds_end": null,
"cds_length": 3573,
"cdna_start": 3776,
"cdna_end": null,
"cdna_length": 4702,
"mane_select": "NM_001940.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATN1",
"gene_hgnc_id": 3033,
"hgvs_c": "c.3188T>G",
"hgvs_p": "p.Leu1063Arg",
"transcript": "ENST00000356654.8",
"protein_id": "ENSP00000349076.3",
"transcript_support_level": 1,
"aa_start": 1063,
"aa_end": null,
"aa_length": 1190,
"cds_start": 3188,
"cds_end": null,
"cds_length": 3573,
"cdna_start": 3425,
"cdna_end": null,
"cdna_length": 4351,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATN1",
"gene_hgnc_id": 3033,
"hgvs_c": "c.3188T>G",
"hgvs_p": "p.Leu1063Arg",
"transcript": "NM_001007026.2",
"protein_id": "NP_001007027.1",
"transcript_support_level": null,
"aa_start": 1063,
"aa_end": null,
"aa_length": 1190,
"cds_start": 3188,
"cds_end": null,
"cds_length": 3573,
"cdna_start": 3429,
"cdna_end": null,
"cdna_length": 4355,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATN1",
"gene_hgnc_id": 3033,
"hgvs_c": "c.3188T>G",
"hgvs_p": "p.Leu1063Arg",
"transcript": "NM_001424176.1",
"protein_id": "NP_001411105.1",
"transcript_support_level": null,
"aa_start": 1063,
"aa_end": null,
"aa_length": 1190,
"cds_start": 3188,
"cds_end": null,
"cds_length": 3573,
"cdna_start": 4087,
"cdna_end": null,
"cdna_length": 5013,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATN1",
"gene_hgnc_id": 3033,
"hgvs_c": "c.3188T>G",
"hgvs_p": "p.Leu1063Arg",
"transcript": "NM_001424177.1",
"protein_id": "NP_001411106.1",
"transcript_support_level": null,
"aa_start": 1063,
"aa_end": null,
"aa_length": 1190,
"cds_start": 3188,
"cds_end": null,
"cds_length": 3573,
"cdna_start": 3760,
"cdna_end": null,
"cdna_length": 4686,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATN1",
"gene_hgnc_id": 3033,
"hgvs_c": "c.3188T>G",
"hgvs_p": "p.Leu1063Arg",
"transcript": "NM_001424178.1",
"protein_id": "NP_001411107.1",
"transcript_support_level": null,
"aa_start": 1063,
"aa_end": null,
"aa_length": 1190,
"cds_start": 3188,
"cds_end": null,
"cds_length": 3573,
"cdna_start": 3592,
"cdna_end": null,
"cdna_length": 4518,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATN1",
"gene_hgnc_id": 3033,
"hgvs_c": "c.3185T>G",
"hgvs_p": "p.Leu1062Arg",
"transcript": "NM_001424179.1",
"protein_id": "NP_001411108.1",
"transcript_support_level": null,
"aa_start": 1062,
"aa_end": null,
"aa_length": 1189,
"cds_start": 3185,
"cds_end": null,
"cds_length": 3570,
"cdna_start": 3410,
"cdna_end": null,
"cdna_length": 4336,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATN1",
"gene_hgnc_id": 3033,
"hgvs_c": "c.3185T>G",
"hgvs_p": "p.Leu1062Arg",
"transcript": "NM_001424180.1",
"protein_id": "NP_001411109.1",
"transcript_support_level": null,
"aa_start": 1062,
"aa_end": null,
"aa_length": 1189,
"cds_start": 3185,
"cds_end": null,
"cds_length": 3570,
"cdna_start": 3773,
"cdna_end": null,
"cdna_length": 4699,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATN1",
"gene_hgnc_id": 3033,
"hgvs_c": "n.45T>G",
"hgvs_p": null,
"transcript": "ENST00000537488.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 899,
"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": "ATN1",
"gene_hgnc_id": 3033,
"hgvs_c": "n.*186T>G",
"hgvs_p": null,
"transcript": "ENST00000541029.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 855,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATN1",
"gene_hgnc_id": 3033,
"dbsnp": "rs1555144360",
"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": 0.8644132614135742,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.536,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9991,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.18,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.918,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.02,
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM1",
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000396684.3",
"gene_symbol": "ATN1",
"hgnc_id": 3033,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3188T>G",
"hgvs_p": "p.Leu1063Arg"
}
],
"clinvar_disease": "Congenital ATN1 related disorder",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Congenital ATN1 related disorder",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}