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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: 17-18277783-TC-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=18277783&ref=TC&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 18277783,
"ref": "TC",
"alt": "T",
"effect": "frameshift_variant",
"transcript": "ENST00000321105.10",
"consequences": [
{
"aa_ref": "R",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOP3A",
"gene_hgnc_id": 11992,
"hgvs_c": "c.2718delG",
"hgvs_p": "p.Thr907fs",
"transcript": "NM_004618.5",
"protein_id": "NP_004609.1",
"transcript_support_level": null,
"aa_start": 906,
"aa_end": null,
"aa_length": 1001,
"cds_start": 2718,
"cds_end": null,
"cds_length": 3006,
"cdna_start": 2934,
"cdna_end": null,
"cdna_length": 6596,
"mane_select": "ENST00000321105.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOP3A",
"gene_hgnc_id": 11992,
"hgvs_c": "c.2718delG",
"hgvs_p": "p.Thr907fs",
"transcript": "ENST00000321105.10",
"protein_id": "ENSP00000321636.5",
"transcript_support_level": 1,
"aa_start": 906,
"aa_end": null,
"aa_length": 1001,
"cds_start": 2718,
"cds_end": null,
"cds_length": 3006,
"cdna_start": 2934,
"cdna_end": null,
"cdna_length": 6596,
"mane_select": "NM_004618.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOP3A",
"gene_hgnc_id": 11992,
"hgvs_c": "c.2643delG",
"hgvs_p": "p.Thr882fs",
"transcript": "ENST00000580095.5",
"protein_id": "ENSP00000462790.1",
"transcript_support_level": 1,
"aa_start": 881,
"aa_end": null,
"aa_length": 975,
"cds_start": 2643,
"cds_end": null,
"cds_length": 2929,
"cdna_start": 2643,
"cdna_end": null,
"cdna_length": 2929,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOP3A",
"gene_hgnc_id": 11992,
"hgvs_c": "c.2433delG",
"hgvs_p": "p.Thr812fs",
"transcript": "NM_001320759.2",
"protein_id": "NP_001307688.1",
"transcript_support_level": null,
"aa_start": 811,
"aa_end": null,
"aa_length": 906,
"cds_start": 2433,
"cds_end": null,
"cds_length": 2721,
"cdna_start": 2860,
"cdna_end": null,
"cdna_length": 6522,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOP3A",
"gene_hgnc_id": 11992,
"hgvs_c": "c.1797delG",
"hgvs_p": "p.Thr600fs",
"transcript": "XM_047436633.1",
"protein_id": "XP_047292589.1",
"transcript_support_level": null,
"aa_start": 599,
"aa_end": null,
"aa_length": 694,
"cds_start": 1797,
"cds_end": null,
"cds_length": 2085,
"cdna_start": 2427,
"cdna_end": null,
"cdna_length": 6089,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOP3A",
"gene_hgnc_id": 11992,
"hgvs_c": "c.1797delG",
"hgvs_p": "p.Thr600fs",
"transcript": "XM_047436634.1",
"protein_id": "XP_047292590.1",
"transcript_support_level": null,
"aa_start": 599,
"aa_end": null,
"aa_length": 694,
"cds_start": 1797,
"cds_end": null,
"cds_length": 2085,
"cdna_start": 2493,
"cdna_end": null,
"cdna_length": 6155,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOP3A",
"gene_hgnc_id": 11992,
"hgvs_c": "n.2073delG",
"hgvs_p": null,
"transcript": "ENST00000469739.6",
"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": 3196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOP3A",
"gene_hgnc_id": 11992,
"hgvs_c": "n.*2374delG",
"hgvs_p": null,
"transcript": "ENST00000582981.5",
"protein_id": "ENSP00000462378.1",
"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": 3239,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOP3A",
"gene_hgnc_id": 11992,
"hgvs_c": "n.*2374delG",
"hgvs_p": null,
"transcript": "ENST00000584582.5",
"protein_id": "ENSP00000462136.1",
"transcript_support_level": 5,
"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": 3661,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOP3A",
"gene_hgnc_id": 11992,
"hgvs_c": "n.*2374delG",
"hgvs_p": null,
"transcript": "ENST00000582981.5",
"protein_id": "ENSP00000462378.1",
"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": 3239,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOP3A",
"gene_hgnc_id": 11992,
"hgvs_c": "n.*2374delG",
"hgvs_p": null,
"transcript": "ENST00000584582.5",
"protein_id": "ENSP00000462136.1",
"transcript_support_level": 5,
"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": 3661,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TOP3A",
"gene_hgnc_id": 11992,
"dbsnp": "rs1288928564",
"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": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.07999999821186066,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": -0.125,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.08,
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "ENST00000321105.10",
"gene_symbol": "TOP3A",
"hgnc_id": 11992,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2718delG",
"hgvs_p": "p.Thr907fs"
}
],
"clinvar_disease": " and increased sister chromatid exchange 2, growth restriction,Microcephaly",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Microcephaly, growth restriction, and increased sister chromatid exchange 2",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}