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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: 5-16545351-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=16545351&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 16545351,
"ref": "T",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000306320.10",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RETREG1",
"gene_hgnc_id": 25964,
"hgvs_c": "c.458+20412A>T",
"hgvs_p": null,
"transcript": "NM_001034850.3",
"protein_id": "NP_001030022.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 497,
"cds_start": -4,
"cds_end": null,
"cds_length": 1494,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3208,
"mane_select": "ENST00000306320.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RETREG1",
"gene_hgnc_id": 25964,
"hgvs_c": "c.458+20412A>T",
"hgvs_p": null,
"transcript": "ENST00000306320.10",
"protein_id": "ENSP00000304642.9",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 497,
"cds_start": -4,
"cds_end": null,
"cds_length": 1494,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3208,
"mane_select": "NM_001034850.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "RETREG1",
"gene_hgnc_id": 25964,
"hgvs_c": "c.614+19267A>T",
"hgvs_p": null,
"transcript": "ENST00000682229.1",
"protein_id": "ENSP00000507342.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 549,
"cds_start": -4,
"cds_end": null,
"cds_length": 1650,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3346,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RETREG1",
"gene_hgnc_id": 25964,
"hgvs_c": "c.458+20412A>T",
"hgvs_p": null,
"transcript": "ENST00000682564.1",
"protein_id": "ENSP00000508099.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 496,
"cds_start": -4,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3184,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "RETREG1",
"gene_hgnc_id": 25964,
"hgvs_c": "c.321-61879A>T",
"hgvs_p": null,
"transcript": "ENST00000684521.1",
"protein_id": "ENSP00000507521.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 451,
"cds_start": -4,
"cds_end": null,
"cds_length": 1356,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2020,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "RETREG1",
"gene_hgnc_id": 25964,
"hgvs_c": "c.125+20412A>T",
"hgvs_p": null,
"transcript": "ENST00000682033.1",
"protein_id": "ENSP00000507240.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 43,
"cds_start": -4,
"cds_end": null,
"cds_length": 132,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 536,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RETREG1",
"gene_hgnc_id": 25964,
"hgvs_c": "n.481+20412A>T",
"hgvs_p": null,
"transcript": "ENST00000682982.1",
"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": 3938,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RETREG1",
"gene_hgnc_id": 25964,
"hgvs_c": "n.484+20412A>T",
"hgvs_p": null,
"transcript": "ENST00000683045.1",
"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": 7708,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RETREG1",
"gene_hgnc_id": 25964,
"hgvs_c": "n.458+20412A>T",
"hgvs_p": null,
"transcript": "ENST00000683527.1",
"protein_id": "ENSP00000507253.1",
"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": 3170,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RETREG1",
"gene_hgnc_id": 25964,
"hgvs_c": "n.476+20412A>T",
"hgvs_p": null,
"transcript": "ENST00000684695.1",
"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": 5434,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RETREG1",
"gene_hgnc_id": 25964,
"hgvs_c": "c.458+20412A>T",
"hgvs_p": null,
"transcript": "XM_011514053.4",
"protein_id": "XP_011512355.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 537,
"cds_start": -4,
"cds_end": null,
"cds_length": 1614,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3328,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RETREG1",
"gene_hgnc_id": 25964,
"dbsnp": "rs1551936",
"frequency_reference_population": 0.000006581545,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.00000658155,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -1.0499999523162842,
"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": -1.05,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.684,
"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": "ENST00000306320.10",
"gene_symbol": "RETREG1",
"hgnc_id": 25964,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.458+20412A>T",
"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
}