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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: 4-54287483-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=54287483&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 54287483,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000257290.10",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.2616C>T",
"hgvs_p": "p.Tyr872Tyr",
"transcript": "NM_006206.6",
"protein_id": "NP_006197.1",
"transcript_support_level": null,
"aa_start": 872,
"aa_end": null,
"aa_length": 1089,
"cds_start": 2616,
"cds_end": null,
"cds_length": 3270,
"cdna_start": 2751,
"cdna_end": null,
"cdna_length": 6378,
"mane_select": "ENST00000257290.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.2616C>T",
"hgvs_p": "p.Tyr872Tyr",
"transcript": "ENST00000257290.10",
"protein_id": "ENSP00000257290.5",
"transcript_support_level": 1,
"aa_start": 872,
"aa_end": null,
"aa_length": 1089,
"cds_start": 2616,
"cds_end": null,
"cds_length": 3270,
"cdna_start": 2751,
"cdna_end": null,
"cdna_length": 6378,
"mane_select": "NM_006206.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000282278",
"gene_hgnc_id": null,
"hgvs_c": "c.1896C>T",
"hgvs_p": "p.Tyr632Tyr",
"transcript": "ENST00000507166.5",
"protein_id": "ENSP00000423325.1",
"transcript_support_level": 2,
"aa_start": 632,
"aa_end": null,
"aa_length": 849,
"cds_start": 1896,
"cds_end": null,
"cds_length": 2550,
"cdna_start": 1896,
"cdna_end": null,
"cdna_length": 2550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.2691C>T",
"hgvs_p": "p.Tyr897Tyr",
"transcript": "NM_001347828.2",
"protein_id": "NP_001334757.1",
"transcript_support_level": null,
"aa_start": 897,
"aa_end": null,
"aa_length": 1114,
"cds_start": 2691,
"cds_end": null,
"cds_length": 3345,
"cdna_start": 2829,
"cdna_end": null,
"cdna_length": 6456,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.2655C>T",
"hgvs_p": "p.Tyr885Tyr",
"transcript": "NM_001347830.2",
"protein_id": "NP_001334759.1",
"transcript_support_level": null,
"aa_start": 885,
"aa_end": null,
"aa_length": 1102,
"cds_start": 2655,
"cds_end": null,
"cds_length": 3309,
"cdna_start": 3167,
"cdna_end": null,
"cdna_length": 6794,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.2616C>T",
"hgvs_p": "p.Tyr872Tyr",
"transcript": "NM_001347829.2",
"protein_id": "NP_001334758.1",
"transcript_support_level": null,
"aa_start": 872,
"aa_end": null,
"aa_length": 1089,
"cds_start": 2616,
"cds_end": null,
"cds_length": 3270,
"cdna_start": 2972,
"cdna_end": null,
"cdna_length": 6599,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.2616C>T",
"hgvs_p": "p.Tyr872Tyr",
"transcript": "XM_005265743.2",
"protein_id": "XP_005265800.1",
"transcript_support_level": null,
"aa_start": 872,
"aa_end": null,
"aa_length": 1089,
"cds_start": 2616,
"cds_end": null,
"cds_length": 3270,
"cdna_start": 3368,
"cdna_end": null,
"cdna_length": 6995,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.2616C>T",
"hgvs_p": "p.Tyr872Tyr",
"transcript": "XM_047415766.1",
"protein_id": "XP_047271722.1",
"transcript_support_level": null,
"aa_start": 872,
"aa_end": null,
"aa_length": 1089,
"cds_start": 2616,
"cds_end": null,
"cds_length": 3270,
"cdna_start": 2831,
"cdna_end": null,
"cdna_length": 6458,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"hgvs_c": "c.2616C>T",
"hgvs_p": "p.Tyr872Tyr",
"transcript": "XM_047415767.1",
"protein_id": "XP_047271723.1",
"transcript_support_level": null,
"aa_start": 872,
"aa_end": null,
"aa_length": 1089,
"cds_start": 2616,
"cds_end": null,
"cds_length": 3270,
"cdna_start": 3134,
"cdna_end": null,
"cdna_length": 6761,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PDGFRA",
"gene_hgnc_id": 8803,
"dbsnp": "rs1060504258",
"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": -0.3499999940395355,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.35,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.352,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Very_Strong,BP7",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 11,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Very_Strong",
"BP7"
],
"verdict": "Benign",
"transcript": "ENST00000257290.10",
"gene_symbol": "PDGFRA",
"hgnc_id": 8803,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "Unknown,AD",
"hgvs_c": "c.2616C>T",
"hgvs_p": "p.Tyr872Tyr"
},
{
"score": -9,
"benign_score": 11,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Very_Strong",
"BP7"
],
"verdict": "Benign",
"transcript": "ENST00000507166.5",
"gene_symbol": "ENSG00000282278",
"hgnc_id": null,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1896C>T",
"hgvs_p": "p.Tyr632Tyr"
}
],
"clinvar_disease": "Gastrointestinal stromal tumor,Hereditary cancer-predisposing syndrome",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "Gastrointestinal stromal tumor|Hereditary cancer-predisposing syndrome",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}