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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: 17-50356715-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=50356715&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 50356715,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000017003.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XYLT2",
"gene_hgnc_id": 15517,
"hgvs_c": "c.1687C>T",
"hgvs_p": "p.Arg563Cys",
"transcript": "NM_022167.4",
"protein_id": "NP_071450.2",
"transcript_support_level": null,
"aa_start": 563,
"aa_end": null,
"aa_length": 865,
"cds_start": 1687,
"cds_end": null,
"cds_length": 2598,
"cdna_start": 1702,
"cdna_end": null,
"cdna_length": 3507,
"mane_select": "ENST00000017003.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XYLT2",
"gene_hgnc_id": 15517,
"hgvs_c": "c.1687C>T",
"hgvs_p": "p.Arg563Cys",
"transcript": "ENST00000017003.7",
"protein_id": "ENSP00000017003.2",
"transcript_support_level": 1,
"aa_start": 563,
"aa_end": null,
"aa_length": 865,
"cds_start": 1687,
"cds_end": null,
"cds_length": 2598,
"cdna_start": 1702,
"cdna_end": null,
"cdna_length": 3507,
"mane_select": "NM_022167.4",
"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": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XYLT2",
"gene_hgnc_id": 15517,
"hgvs_c": "n.1687C>T",
"hgvs_p": null,
"transcript": "ENST00000376550.7",
"protein_id": "ENSP00000365733.3",
"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": 3267,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XYLT2",
"gene_hgnc_id": 15517,
"hgvs_c": "c.1687C>T",
"hgvs_p": "p.Arg563Cys",
"transcript": "ENST00000507602.5",
"protein_id": "ENSP00000426501.1",
"transcript_support_level": 2,
"aa_start": 563,
"aa_end": null,
"aa_length": 676,
"cds_start": 1687,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 1693,
"cdna_end": null,
"cdna_length": 2107,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XYLT2",
"gene_hgnc_id": 15517,
"hgvs_c": "c.1591C>T",
"hgvs_p": "p.Arg531Cys",
"transcript": "XM_005257572.5",
"protein_id": "XP_005257629.1",
"transcript_support_level": null,
"aa_start": 531,
"aa_end": null,
"aa_length": 833,
"cds_start": 1591,
"cds_end": null,
"cds_length": 2502,
"cdna_start": 2110,
"cdna_end": null,
"cdna_length": 3915,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XYLT2",
"gene_hgnc_id": 15517,
"hgvs_c": "c.1096C>T",
"hgvs_p": "p.Arg366Cys",
"transcript": "XM_047436522.1",
"protein_id": "XP_047292478.1",
"transcript_support_level": null,
"aa_start": 366,
"aa_end": null,
"aa_length": 668,
"cds_start": 1096,
"cds_end": null,
"cds_length": 2007,
"cdna_start": 6622,
"cdna_end": null,
"cdna_length": 8427,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XYLT2",
"gene_hgnc_id": 15517,
"hgvs_c": "n.283C>T",
"hgvs_p": null,
"transcript": "ENST00000511654.1",
"protein_id": "ENSP00000428350.1",
"transcript_support_level": 3,
"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": 587,
"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": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XYLT2",
"gene_hgnc_id": 15517,
"hgvs_c": "n.1702C>T",
"hgvs_p": null,
"transcript": "NR_110010.2",
"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": 3311,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "XYLT2",
"gene_hgnc_id": 15517,
"dbsnp": "rs150417924",
"frequency_reference_population": 0.0000031049306,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000205744,
"gnomad_genomes_af": 0.0000131387,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8874310255050659,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.455,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5847,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.05,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 1.742,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Moderate,PP5_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000017003.7",
"gene_symbol": "XYLT2",
"hgnc_id": 15517,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1687C>T",
"hgvs_p": "p.Arg563Cys"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}