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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: 12-101760044-A-AGTAG (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=101760044&ref=A&alt=AGTAG&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 101760044,
"ref": "A",
"alt": "AGTAG",
"effect": "frameshift_variant",
"transcript": "ENST00000299314.12",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "YL?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"hgvs_c": "c.3231_3234dupCTAC",
"hgvs_p": "p.Tyr1079fs",
"transcript": "NM_024312.5",
"protein_id": "NP_077288.2",
"transcript_support_level": null,
"aa_start": 1078,
"aa_end": null,
"aa_length": 1256,
"cds_start": 3234,
"cds_end": null,
"cds_length": 3771,
"cdna_start": 3518,
"cdna_end": null,
"cdna_length": 5720,
"mane_select": "ENST00000299314.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "YL?",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"hgvs_c": "c.3231_3234dupCTAC",
"hgvs_p": "p.Tyr1079fs",
"transcript": "ENST00000299314.12",
"protein_id": "ENSP00000299314.7",
"transcript_support_level": 1,
"aa_start": 1078,
"aa_end": null,
"aa_length": 1256,
"cds_start": 3234,
"cds_end": null,
"cds_length": 3771,
"cdna_start": 3518,
"cdna_end": null,
"cdna_length": 5720,
"mane_select": "NM_024312.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "YL?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"hgvs_c": "c.42_45dupCTAC",
"hgvs_p": "p.Tyr16fs",
"transcript": "ENST00000550718.1",
"protein_id": "ENSP00000449557.1",
"transcript_support_level": 3,
"aa_start": 15,
"aa_end": null,
"aa_length": 116,
"cds_start": 45,
"cds_end": null,
"cds_length": 351,
"cdna_start": 46,
"cdna_end": null,
"cdna_length": 598,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "YL?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"hgvs_c": "c.3150_3153dupCTAC",
"hgvs_p": "p.Tyr1052fs",
"transcript": "XM_011538731.3",
"protein_id": "XP_011537033.1",
"transcript_support_level": null,
"aa_start": 1051,
"aa_end": null,
"aa_length": 1229,
"cds_start": 3153,
"cds_end": null,
"cds_length": 3690,
"cdna_start": 3169,
"cdna_end": null,
"cdna_length": 5371,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "YL?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"hgvs_c": "c.3231_3234dupCTAC",
"hgvs_p": "p.Tyr1079fs",
"transcript": "XM_006719593.4",
"protein_id": "XP_006719656.1",
"transcript_support_level": null,
"aa_start": 1078,
"aa_end": null,
"aa_length": 1179,
"cds_start": 3234,
"cds_end": null,
"cds_length": 3540,
"cdna_start": 3518,
"cdna_end": null,
"cdna_length": 4070,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"hgvs_c": "n.97_100dupCTAC",
"hgvs_p": null,
"transcript": "ENST00000549194.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 570,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"dbsnp": "rs34256381",
"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": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 1.763,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000299314.12",
"gene_symbol": "GNPTAB",
"hgnc_id": 29670,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3231_3234dupCTAC",
"hgvs_p": "p.Tyr1079fs"
}
],
"clinvar_disease": "Mucolipidosis type II",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Mucolipidosis type II",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}