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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: 4-15587928-AG-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=15587928&ref=AG&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 15587928,
"ref": "AG",
"alt": "A",
"effect": "splice_donor_variant,intron_variant",
"transcript": "ENST00000424120.6",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": 32,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.4179+1delG",
"hgvs_p": null,
"transcript": "NM_001378615.1",
"protein_id": "NP_001365544.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1620,
"cds_start": -4,
"cds_end": null,
"cds_length": 4863,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5184,
"mane_select": "ENST00000424120.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": 32,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.4179+1delG",
"hgvs_p": null,
"transcript": "ENST00000424120.6",
"protein_id": "ENSP00000403465.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1620,
"cds_start": -4,
"cds_end": null,
"cds_length": 4863,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5184,
"mane_select": "NM_001378615.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": 33,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.4179+1delG",
"hgvs_p": null,
"transcript": "ENST00000503292.6",
"protein_id": "ENSP00000421809.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1620,
"cds_start": -4,
"cds_end": null,
"cds_length": 4863,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5226,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": 29,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.4032+1delG",
"hgvs_p": null,
"transcript": "ENST00000634028.2",
"protein_id": "ENSP00000488669.2",
"transcript_support_level": 1,
"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": 4784,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": 33,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.4215+1delG",
"hgvs_p": null,
"transcript": "ENST00000389652.11",
"protein_id": "ENSP00000374303.8",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1632,
"cds_start": -4,
"cds_end": null,
"cds_length": 4899,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5044,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": 33,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.4179+1delG",
"hgvs_p": null,
"transcript": "NM_001080522.2",
"protein_id": "NP_001073991.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1620,
"cds_start": -4,
"cds_end": null,
"cds_length": 4863,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5240,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": 30,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.4032+1delG",
"hgvs_p": null,
"transcript": "NM_001378617.1",
"protein_id": "NP_001365546.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1571,
"cds_start": -4,
"cds_end": null,
"cds_length": 4716,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4984,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": 30,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.4032+1delG",
"hgvs_p": null,
"transcript": "ENST00000506643.5",
"protein_id": "ENSP00000422931.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 1571,
"cds_start": -4,
"cds_end": null,
"cds_length": 4716,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4989,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": 29,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.3855+1delG",
"hgvs_p": null,
"transcript": "ENST00000674945.1",
"protein_id": "ENSP00000502333.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1512,
"cds_start": -4,
"cds_end": null,
"cds_length": 4539,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4809,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.408+1delG",
"hgvs_p": null,
"transcript": "ENST00000514039.6",
"protein_id": "ENSP00000488534.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 322,
"cds_start": -4,
"cds_end": null,
"cds_length": 969,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 969,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": 31,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.*1676+1delG",
"hgvs_p": null,
"transcript": "ENST00000650860.2",
"protein_id": "ENSP00000498775.1",
"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": 5513,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.1399+1delG",
"hgvs_p": null,
"transcript": "ENST00000675768.1",
"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": 2447,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.4838+1delG",
"hgvs_p": null,
"transcript": "ENST00000680586.1",
"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": 6514,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"dbsnp": "rs386833760",
"frequency_reference_population": 0.00007667701,
"hom_count_reference_population": 0,
"allele_count_reference_population": 121,
"gnomad_exomes_af": 0.0000652269,
"gnomad_genomes_af": 0.000183901,
"gnomad_exomes_ac": 93,
"gnomad_genomes_ac": 28,
"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": 0.8299999833106995,
"splice_prediction_selected": "Pathogenic",
"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": 8.112,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.83,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PVS1_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000424120.6",
"gene_symbol": "CC2D2A",
"hgnc_id": 29253,
"effects": [
"splice_donor_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.4179+1delG",
"hgvs_p": null
}
],
"clinvar_disease": " type 6,7 conditions,Anencephaly,COACH syndrome 2,Inborn genetic diseases,Joubert syndrome,Joubert syndrome 9,Meckel syndrome,Meckel-Gruber syndrome,Polydactyly,Renal cyst,Retinitis pigmentosa 93,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:10",
"phenotype_combined": "Meckel syndrome, type 6|Joubert syndrome 9|7 conditions|Joubert syndrome;Meckel-Gruber syndrome|not provided|Polydactyly;Renal cyst;Anencephaly|Meckel-Gruber syndrome|Joubert syndrome 9;COACH syndrome 2;Meckel syndrome, type 6;Retinitis pigmentosa 93|Inborn genetic diseases",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}