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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: 7-138091822-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=138091822&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 138091822,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000242375.8",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AKR1D1",
"gene_hgnc_id": 388,
"hgvs_c": "c.316C>T",
"hgvs_p": "p.Leu106Phe",
"transcript": "NM_005989.4",
"protein_id": "NP_005980.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 326,
"cds_start": 316,
"cds_end": null,
"cds_length": 981,
"cdna_start": 376,
"cdna_end": null,
"cdna_length": 2684,
"mane_select": "ENST00000242375.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AKR1D1",
"gene_hgnc_id": 388,
"hgvs_c": "c.316C>T",
"hgvs_p": "p.Leu106Phe",
"transcript": "ENST00000242375.8",
"protein_id": "ENSP00000242375.3",
"transcript_support_level": 1,
"aa_start": 106,
"aa_end": null,
"aa_length": 326,
"cds_start": 316,
"cds_end": null,
"cds_length": 981,
"cdna_start": 376,
"cdna_end": null,
"cdna_length": 2684,
"mane_select": "NM_005989.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AKR1D1",
"gene_hgnc_id": 388,
"hgvs_c": "c.316C>T",
"hgvs_p": "p.Leu106Phe",
"transcript": "NM_001190907.2",
"protein_id": "NP_001177836.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 290,
"cds_start": 316,
"cds_end": null,
"cds_length": 873,
"cdna_start": 376,
"cdna_end": null,
"cdna_length": 2601,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AKR1D1",
"gene_hgnc_id": 388,
"hgvs_c": "c.316C>T",
"hgvs_p": "p.Leu106Phe",
"transcript": "ENST00000432161.5",
"protein_id": "ENSP00000389197.1",
"transcript_support_level": 2,
"aa_start": 106,
"aa_end": null,
"aa_length": 290,
"cds_start": 316,
"cds_end": null,
"cds_length": 873,
"cdna_start": 403,
"cdna_end": null,
"cdna_length": 1236,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AKR1D1",
"gene_hgnc_id": 388,
"hgvs_c": "c.316C>T",
"hgvs_p": "p.Leu106Phe",
"transcript": "NM_001190906.2",
"protein_id": "NP_001177835.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 285,
"cds_start": 316,
"cds_end": null,
"cds_length": 858,
"cdna_start": 376,
"cdna_end": null,
"cdna_length": 2561,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AKR1D1",
"gene_hgnc_id": 388,
"hgvs_c": "c.316C>T",
"hgvs_p": "p.Leu106Phe",
"transcript": "ENST00000411726.6",
"protein_id": "ENSP00000402374.2",
"transcript_support_level": 2,
"aa_start": 106,
"aa_end": null,
"aa_length": 285,
"cds_start": 316,
"cds_end": null,
"cds_length": 858,
"cdna_start": 368,
"cdna_end": null,
"cdna_length": 2234,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AKR1D1",
"gene_hgnc_id": 388,
"hgvs_c": "c.148C>T",
"hgvs_p": "p.Leu50Phe",
"transcript": "ENST00000438242.1",
"protein_id": "ENSP00000397042.1",
"transcript_support_level": 3,
"aa_start": 50,
"aa_end": null,
"aa_length": 95,
"cds_start": 148,
"cds_end": null,
"cds_length": 289,
"cdna_start": 149,
"cdna_end": null,
"cdna_length": 290,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AKR1D1",
"gene_hgnc_id": 388,
"hgvs_c": "c.148C>T",
"hgvs_p": "p.Leu50Phe",
"transcript": "XM_047420763.1",
"protein_id": "XP_047276719.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 270,
"cds_start": 148,
"cds_end": null,
"cds_length": 813,
"cdna_start": 208,
"cdna_end": null,
"cdna_length": 2516,
"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": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AKR1D1",
"gene_hgnc_id": 388,
"hgvs_c": "n.226C>T",
"hgvs_p": null,
"transcript": "ENST00000468877.2",
"protein_id": null,
"transcript_support_level": 2,
"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": 1208,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000308006",
"gene_hgnc_id": null,
"hgvs_c": "n.255-4624G>A",
"hgvs_p": null,
"transcript": "ENST00000830395.1",
"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": 379,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AKR1D1",
"gene_hgnc_id": 388,
"hgvs_c": "n.-21C>T",
"hgvs_p": null,
"transcript": "ENST00000470851.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 487,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "AKR1D1",
"gene_hgnc_id": 388,
"dbsnp": "rs121918343",
"frequency_reference_population": 0.0000020522082,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205221,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9796100854873657,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.485,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8737,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.21,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.034,
"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": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PP2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000242375.8",
"gene_symbol": "AKR1D1",
"hgnc_id": 388,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.316C>T",
"hgvs_p": "p.Leu106Phe"
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000830395.1",
"gene_symbol": "ENSG00000308006",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.255-4624G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Congenital bile acid synthesis defect 2",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Congenital bile acid synthesis defect 2",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}