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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: 12-6867538-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=6867538&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 6867538,
"ref": "C",
"alt": "T",
"effect": "5_prime_UTR_premature_start_codon_gain_variant",
"transcript": "NM_000365.6",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPI1",
"gene_hgnc_id": 12009,
"hgvs_c": "c.-29C>T",
"hgvs_p": null,
"transcript": "NM_000365.6",
"protein_id": "NP_000356.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 249,
"cds_start": -4,
"cds_end": null,
"cds_length": 750,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1351,
"mane_select": "ENST00000396705.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPI1",
"gene_hgnc_id": 12009,
"hgvs_c": "c.-29C>T",
"hgvs_p": null,
"transcript": "ENST00000396705.10",
"protein_id": "ENSP00000379933.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 249,
"cds_start": -4,
"cds_end": null,
"cds_length": 750,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1351,
"mane_select": "NM_000365.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPI1",
"gene_hgnc_id": 12009,
"hgvs_c": "c.83C>T",
"hgvs_p": "p.Thr28Ile",
"transcript": "ENST00000229270.8",
"protein_id": "ENSP00000229270.4",
"transcript_support_level": 1,
"aa_start": 28,
"aa_end": null,
"aa_length": 286,
"cds_start": 83,
"cds_end": null,
"cds_length": 861,
"cdna_start": 420,
"cdna_end": null,
"cdna_length": 1763,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPI1",
"gene_hgnc_id": 12009,
"hgvs_c": "c.83C>T",
"hgvs_p": "p.Thr28Ile",
"transcript": "ENST00000613953.4",
"protein_id": "ENSP00000484435.1",
"transcript_support_level": 1,
"aa_start": 28,
"aa_end": null,
"aa_length": 286,
"cds_start": 83,
"cds_end": null,
"cds_length": 861,
"cdna_start": 119,
"cdna_end": null,
"cdna_length": 1460,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPI1",
"gene_hgnc_id": 12009,
"hgvs_c": "c.-29C>T",
"hgvs_p": null,
"transcript": "NM_000365.6",
"protein_id": "NP_000356.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 249,
"cds_start": -4,
"cds_end": null,
"cds_length": 750,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1351,
"mane_select": "ENST00000396705.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPI1",
"gene_hgnc_id": 12009,
"hgvs_c": "c.-29C>T",
"hgvs_p": null,
"transcript": "ENST00000396705.10",
"protein_id": "ENSP00000379933.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 249,
"cds_start": -4,
"cds_end": null,
"cds_length": 750,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1351,
"mane_select": "NM_000365.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPI1",
"gene_hgnc_id": 12009,
"hgvs_c": "c.83C>T",
"hgvs_p": "p.Thr28Ile",
"transcript": "NM_001159287.1",
"protein_id": "NP_001152759.1",
"transcript_support_level": null,
"aa_start": 28,
"aa_end": null,
"aa_length": 286,
"cds_start": 83,
"cds_end": null,
"cds_length": 861,
"cdna_start": 119,
"cdna_end": null,
"cdna_length": 1460,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TPI1",
"gene_hgnc_id": 12009,
"dbsnp": "rs181882616",
"frequency_reference_population": 0.0000149208445,
"hom_count_reference_population": 0,
"allele_count_reference_population": 24,
"gnomad_exomes_af": 0.0000144204,
"gnomad_genomes_af": 0.0000197083,
"gnomad_exomes_ac": 21,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.08500614762306213,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.024,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.45,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.034,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000365.6",
"gene_symbol": "TPI1",
"hgnc_id": 12009,
"effects": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-29C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Triosephosphate isomerase deficiency",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Triosephosphate isomerase deficiency",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}