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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: 2-48597362-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=48597362&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 48597362,
"ref": "C",
"alt": "A",
"effect": "3_prime_UTR_variant",
"transcript": "ENST00000404752.6",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STON1",
"gene_hgnc_id": 17003,
"hgvs_c": "c.*2060C>A",
"hgvs_p": null,
"transcript": "NM_006873.4",
"protein_id": "NP_006864.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 735,
"cds_start": -4,
"cds_end": null,
"cds_length": 2208,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5529,
"mane_select": "ENST00000404752.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STON1",
"gene_hgnc_id": 17003,
"hgvs_c": "c.*2060C>A",
"hgvs_p": null,
"transcript": "ENST00000404752.6",
"protein_id": "ENSP00000385273.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 735,
"cds_start": -4,
"cds_end": null,
"cds_length": 2208,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5529,
"mane_select": "NM_006873.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STON1",
"gene_hgnc_id": 17003,
"hgvs_c": "c.*2060C>A",
"hgvs_p": null,
"transcript": "ENST00000406226.1",
"protein_id": "ENSP00000384615.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 735,
"cds_start": -4,
"cds_end": null,
"cds_length": 2208,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5614,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "STON1-GTF2A1L",
"gene_hgnc_id": 30651,
"hgvs_c": "c.2133+5507C>A",
"hgvs_p": null,
"transcript": "ENST00000394754.5",
"protein_id": "ENSP00000378236.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1182,
"cds_start": -4,
"cds_end": null,
"cds_length": 3549,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3824,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "STON1-GTF2A1L",
"gene_hgnc_id": 30651,
"hgvs_c": "c.2133+5507C>A",
"hgvs_p": null,
"transcript": "ENST00000394751.5",
"protein_id": "ENSP00000378234.3",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 1135,
"cds_start": -4,
"cds_end": null,
"cds_length": 3408,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3534,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STON1",
"gene_hgnc_id": 17003,
"hgvs_c": "c.*2060C>A",
"hgvs_p": null,
"transcript": "NM_001198595.2",
"protein_id": "NP_001185524.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 735,
"cds_start": -4,
"cds_end": null,
"cds_length": 2208,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5646,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STON1",
"gene_hgnc_id": 17003,
"hgvs_c": "c.*2060C>A",
"hgvs_p": null,
"transcript": "ENST00000649748.1",
"protein_id": "ENSP00000497745.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 735,
"cds_start": -4,
"cds_end": null,
"cds_length": 2208,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5606,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "STON1-GTF2A1L",
"gene_hgnc_id": 30651,
"hgvs_c": "c.2133+5507C>A",
"hgvs_p": null,
"transcript": "NM_172311.3",
"protein_id": "NP_758515.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1182,
"cds_start": -4,
"cds_end": null,
"cds_length": 3549,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4067,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "STON1-GTF2A1L",
"gene_hgnc_id": 30651,
"hgvs_c": "c.2133+5507C>A",
"hgvs_p": null,
"transcript": "ENST00000405008.5",
"protein_id": "ENSP00000385499.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1182,
"cds_start": -4,
"cds_end": null,
"cds_length": 3549,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3821,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "STON1-GTF2A1L",
"gene_hgnc_id": 30651,
"hgvs_c": "c.2133+5507C>A",
"hgvs_p": null,
"transcript": "NM_001198593.2",
"protein_id": "NP_001185522.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1158,
"cds_start": -4,
"cds_end": null,
"cds_length": 3477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3792,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "STON1-GTF2A1L",
"gene_hgnc_id": 30651,
"hgvs_c": "c.2133+5507C>A",
"hgvs_p": null,
"transcript": "ENST00000402114.6",
"protein_id": "ENSP00000385701.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 1158,
"cds_start": -4,
"cds_end": null,
"cds_length": 3477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3790,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "STON1-GTF2A1L",
"gene_hgnc_id": 30651,
"hgvs_c": "c.2133+5507C>A",
"hgvs_p": null,
"transcript": "NM_001198594.1",
"protein_id": "NP_001185523.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1135,
"cds_start": -4,
"cds_end": null,
"cds_length": 3408,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3622,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "STON1",
"gene_hgnc_id": 17003,
"dbsnp": "rs3749146",
"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": -0.8700000047683716,
"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": -0.87,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.809,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000404752.6",
"gene_symbol": "STON1",
"hgnc_id": 17003,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*2060C>A",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000394751.5",
"gene_symbol": "STON1-GTF2A1L",
"hgnc_id": 30651,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.2133+5507C>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}