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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: 2-227164755-AGGTGCTCCTGCTGCCGCTCCTGCT-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=227164755&ref=AGGTGCTCCTGCTGCCGCTCCTGCT&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 227164755,
"ref": "AGGTGCTCCTGCTGCCGCTCCTGCT",
"alt": "A",
"effect": "conservative_inframe_deletion",
"transcript": "ENST00000396578.8",
"consequences": [
{
"aa_ref": "LPLLLVLL",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "c.40_63delCTGCCGCTCCTGCTGGTGCTCCTG",
"hgvs_p": "p.Leu14_Leu21del",
"transcript": "NM_000091.5",
"protein_id": "NP_000082.2",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 1670,
"cds_start": 40,
"cds_end": null,
"cds_length": 5013,
"cdna_start": 143,
"cdna_end": null,
"cdna_length": 8038,
"mane_select": "ENST00000396578.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LPLLLVLL",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "c.40_63delCTGCCGCTCCTGCTGGTGCTCCTG",
"hgvs_p": "p.Leu14_Leu21del",
"transcript": "ENST00000396578.8",
"protein_id": "ENSP00000379823.3",
"transcript_support_level": 1,
"aa_start": 14,
"aa_end": null,
"aa_length": 1670,
"cds_start": 40,
"cds_end": null,
"cds_length": 5013,
"cdna_start": 143,
"cdna_end": null,
"cdna_length": 8038,
"mane_select": "NM_000091.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LPLLLVLL",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "c.40_63delCTGCCGCTCCTGCTGGTGCTCCTG",
"hgvs_p": "p.Leu14_Leu21del",
"transcript": "XM_005246277.4",
"protein_id": "XP_005246334.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 1635,
"cds_start": 40,
"cds_end": null,
"cds_length": 4908,
"cdna_start": 143,
"cdna_end": null,
"cdna_length": 7933,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LPLLLVLL",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "c.40_63delCTGCCGCTCCTGCTGGTGCTCCTG",
"hgvs_p": "p.Leu14_Leu21del",
"transcript": "XM_011510555.2",
"protein_id": "XP_011508857.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 1609,
"cds_start": 40,
"cds_end": null,
"cds_length": 4830,
"cdna_start": 143,
"cdna_end": null,
"cdna_length": 5012,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LPLLLVLL",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "c.40_63delCTGCCGCTCCTGCTGGTGCTCCTG",
"hgvs_p": "p.Leu14_Leu21del",
"transcript": "XM_047443224.1",
"protein_id": "XP_047299180.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 1498,
"cds_start": 40,
"cds_end": null,
"cds_length": 4497,
"cdna_start": 143,
"cdna_end": null,
"cdna_length": 4677,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LPLLLVLL",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "c.40_63delCTGCCGCTCCTGCTGGTGCTCCTG",
"hgvs_p": "p.Leu14_Leu21del",
"transcript": "XM_006712245.4",
"protein_id": "XP_006712308.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 1189,
"cds_start": 40,
"cds_end": null,
"cds_length": 3570,
"cdna_start": 143,
"cdna_end": null,
"cdna_length": 3759,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LPLLLVLL",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "c.40_63delCTGCCGCTCCTGCTGGTGCTCCTG",
"hgvs_p": "p.Leu14_Leu21del",
"transcript": "XM_017003295.2",
"protein_id": "XP_016858784.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 1119,
"cds_start": 40,
"cds_end": null,
"cds_length": 3360,
"cdna_start": 143,
"cdna_end": null,
"cdna_length": 3898,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LPLLLVLL",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "c.40_63delCTGCCGCTCCTGCTGGTGCTCCTG",
"hgvs_p": "p.Leu14_Leu21del",
"transcript": "XM_005246280.4",
"protein_id": "XP_005246337.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 1051,
"cds_start": 40,
"cds_end": null,
"cds_length": 3156,
"cdna_start": 143,
"cdna_end": null,
"cdna_length": 3357,
"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": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "n.143_166delCTGCCGCTCCTGCTGGTGCTCCTG",
"hgvs_p": null,
"transcript": "XR_001738601.2",
"protein_id": null,
"transcript_support_level": null,
"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": 4938,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"dbsnp": "rs876657397",
"frequency_reference_population": 0.00005570994,
"hom_count_reference_population": 0,
"allele_count_reference_population": 85,
"gnomad_exomes_af": 0.0000596883,
"gnomad_genomes_af": 0.0000197426,
"gnomad_exomes_ac": 82,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"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": 0.454,
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PP5_Very_Strong,BP3",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 1,
"pathogenic_score": 8,
"criteria": [
"PP5_Very_Strong",
"BP3"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000396578.8",
"gene_symbol": "COL4A3",
"hgnc_id": 2204,
"effects": [
"conservative_inframe_deletion"
],
"inheritance_mode": "AD,AR,SD",
"hgvs_c": "c.40_63delCTGCCGCTCCTGCTGGTGCTCCTG",
"hgvs_p": "p.Leu14_Leu21del"
}
],
"clinvar_disease": " 2, autosomal recessive, benign familial,Alport syndrome,Alport syndrome 3b,Autosomal dominant Alport syndrome,Autosomal recessive Alport syndrome,COL4A3-related disorder,Hematuria,Inborn genetic diseases,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:8",
"phenotype_combined": "Autosomal recessive Alport syndrome|not provided|Alport syndrome|Inborn genetic diseases|Autosomal dominant Alport syndrome;Hematuria, benign familial, 2;Alport syndrome 3b, autosomal recessive|COL4A3-related disorder",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}