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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: 1-53510022-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=53510022&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 53510022,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000628545.2",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLIS1",
"gene_hgnc_id": 29525,
"hgvs_c": "c.1889G>A",
"hgvs_p": "p.Gly630Glu",
"transcript": "NM_001367484.1",
"protein_id": "NP_001354413.1",
"transcript_support_level": null,
"aa_start": 630,
"aa_end": null,
"aa_length": 795,
"cds_start": 1889,
"cds_end": null,
"cds_length": 2388,
"cdna_start": 1991,
"cdna_end": null,
"cdna_length": 2870,
"mane_select": "ENST00000628545.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLIS1",
"gene_hgnc_id": 29525,
"hgvs_c": "c.1889G>A",
"hgvs_p": "p.Gly630Glu",
"transcript": "ENST00000628545.2",
"protein_id": "ENSP00000486112.1",
"transcript_support_level": 5,
"aa_start": 630,
"aa_end": null,
"aa_length": 795,
"cds_start": 1889,
"cds_end": null,
"cds_length": 2388,
"cdna_start": 1991,
"cdna_end": null,
"cdna_length": 2870,
"mane_select": "NM_001367484.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLIS1",
"gene_hgnc_id": 29525,
"hgvs_c": "c.1913G>A",
"hgvs_p": "p.Gly638Glu",
"transcript": "NM_001390836.1",
"protein_id": "NP_001377765.1",
"transcript_support_level": null,
"aa_start": 638,
"aa_end": null,
"aa_length": 803,
"cds_start": 1913,
"cds_end": null,
"cds_length": 2412,
"cdna_start": 2015,
"cdna_end": null,
"cdna_length": 2894,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLIS1",
"gene_hgnc_id": 29525,
"hgvs_c": "c.1889G>A",
"hgvs_p": "p.Gly630Glu",
"transcript": "NM_001390837.1",
"protein_id": "NP_001377766.1",
"transcript_support_level": null,
"aa_start": 630,
"aa_end": null,
"aa_length": 795,
"cds_start": 1889,
"cds_end": null,
"cds_length": 2388,
"cdna_start": 2019,
"cdna_end": null,
"cdna_length": 2898,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLIS1",
"gene_hgnc_id": 29525,
"hgvs_c": "c.1889G>A",
"hgvs_p": "p.Gly630Glu",
"transcript": "NM_001390838.1",
"protein_id": "NP_001377767.1",
"transcript_support_level": null,
"aa_start": 630,
"aa_end": null,
"aa_length": 739,
"cds_start": 1889,
"cds_end": null,
"cds_length": 2220,
"cdna_start": 1991,
"cdna_end": null,
"cdna_length": 2702,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLIS1",
"gene_hgnc_id": 29525,
"hgvs_c": "c.1364G>A",
"hgvs_p": "p.Gly455Glu",
"transcript": "NM_147193.4",
"protein_id": "NP_671726.2",
"transcript_support_level": null,
"aa_start": 455,
"aa_end": null,
"aa_length": 620,
"cds_start": 1364,
"cds_end": null,
"cds_length": 1863,
"cdna_start": 1930,
"cdna_end": null,
"cdna_length": 2809,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLIS1",
"gene_hgnc_id": 29525,
"hgvs_c": "c.1364G>A",
"hgvs_p": "p.Gly455Glu",
"transcript": "ENST00000312233.4",
"protein_id": "ENSP00000309653.2",
"transcript_support_level": 2,
"aa_start": 455,
"aa_end": null,
"aa_length": 620,
"cds_start": 1364,
"cds_end": null,
"cds_length": 1863,
"cdna_start": 1931,
"cdna_end": null,
"cdna_length": 2812,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLIS1",
"gene_hgnc_id": 29525,
"hgvs_c": "c.1877G>A",
"hgvs_p": "p.Gly626Glu",
"transcript": "XM_017000409.2",
"protein_id": "XP_016855898.1",
"transcript_support_level": null,
"aa_start": 626,
"aa_end": null,
"aa_length": 791,
"cds_start": 1877,
"cds_end": null,
"cds_length": 2376,
"cdna_start": 1979,
"cdna_end": null,
"cdna_length": 2858,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLIS1",
"gene_hgnc_id": 29525,
"hgvs_c": "c.1877G>A",
"hgvs_p": "p.Gly626Glu",
"transcript": "XM_047447071.1",
"protein_id": "XP_047303027.1",
"transcript_support_level": null,
"aa_start": 626,
"aa_end": null,
"aa_length": 791,
"cds_start": 1877,
"cds_end": null,
"cds_length": 2376,
"cdna_start": 2977,
"cdna_end": null,
"cdna_length": 3856,
"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": 8,
"intron_rank_end": null,
"gene_symbol": "GLIS1",
"gene_hgnc_id": 29525,
"hgvs_c": "c.1884-3246G>A",
"hgvs_p": null,
"transcript": "XM_017000411.2",
"protein_id": "XP_016855900.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 629,
"cds_start": -4,
"cds_end": null,
"cds_length": 1890,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2523,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLIS1",
"gene_hgnc_id": 29525,
"hgvs_c": "c.*2868G>A",
"hgvs_p": null,
"transcript": "XM_047447085.1",
"protein_id": "XP_047303041.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 638,
"cds_start": -4,
"cds_end": null,
"cds_length": 1917,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4785,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLIS1",
"gene_hgnc_id": 29525,
"hgvs_c": "c.*2868G>A",
"hgvs_p": null,
"transcript": "XM_047447086.1",
"protein_id": "XP_047303042.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 638,
"cds_start": -4,
"cds_end": null,
"cds_length": 1917,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4757,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GLIS1",
"gene_hgnc_id": 29525,
"dbsnp": "rs982751743",
"frequency_reference_population": 0.000023675251,
"hom_count_reference_population": 0,
"allele_count_reference_population": 30,
"gnomad_exomes_af": 0.0000260085,
"gnomad_genomes_af": 0.0000065735,
"gnomad_exomes_ac": 29,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2055913805961609,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.093,
"revel_prediction": "Benign",
"alphamissense_score": 0.2687,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.44,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.68,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000628545.2",
"gene_symbol": "GLIS1",
"hgnc_id": 29525,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1889G>A",
"hgvs_p": "p.Gly630Glu"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}