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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: 6-87506443-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=87506443&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 87506443,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000369552.9",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A1",
"gene_hgnc_id": 11021,
"hgvs_c": "c.569T>C",
"hgvs_p": "p.Phe190Ser",
"transcript": "NM_006416.5",
"protein_id": "NP_006407.1",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 337,
"cds_start": 569,
"cds_end": null,
"cds_length": 1014,
"cdna_start": 599,
"cdna_end": null,
"cdna_length": 1854,
"mane_select": "ENST00000369552.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A1",
"gene_hgnc_id": 11021,
"hgvs_c": "c.569T>C",
"hgvs_p": "p.Phe190Ser",
"transcript": "ENST00000369552.9",
"protein_id": "ENSP00000358565.4",
"transcript_support_level": 1,
"aa_start": 190,
"aa_end": null,
"aa_length": 337,
"cds_start": 569,
"cds_end": null,
"cds_length": 1014,
"cdna_start": 599,
"cdna_end": null,
"cdna_length": 1854,
"mane_select": "NM_006416.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A1",
"gene_hgnc_id": 11021,
"hgvs_c": "c.569T>C",
"hgvs_p": "p.Phe190Ser",
"transcript": "ENST00000369556.7",
"protein_id": "ENSP00000358569.3",
"transcript_support_level": 1,
"aa_start": 190,
"aa_end": null,
"aa_length": 278,
"cds_start": 569,
"cds_end": null,
"cds_length": 837,
"cdna_start": 648,
"cdna_end": null,
"cdna_length": 1720,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A1",
"gene_hgnc_id": 11021,
"hgvs_c": "c.569T>C",
"hgvs_p": "p.Phe190Ser",
"transcript": "NM_001168398.2",
"protein_id": "NP_001161870.1",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 278,
"cds_start": 569,
"cds_end": null,
"cds_length": 837,
"cdna_start": 599,
"cdna_end": null,
"cdna_length": 1677,
"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": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000213204",
"gene_hgnc_id": null,
"hgvs_c": "n.1108T>C",
"hgvs_p": null,
"transcript": "ENST00000506888.5",
"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": 1842,
"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": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "SLC35A1",
"gene_hgnc_id": 11021,
"hgvs_c": "c.508-2598T>C",
"hgvs_p": null,
"transcript": "ENST00000369557.9",
"protein_id": "ENSP00000358570.5",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 189,
"cds_start": -4,
"cds_end": null,
"cds_length": 570,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1653,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "SLC35A1",
"gene_hgnc_id": 11021,
"hgvs_c": "n.583-1977T>C",
"hgvs_p": null,
"transcript": "ENST00000464978.5",
"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": 1299,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC35A1",
"gene_hgnc_id": 11021,
"dbsnp": "rs763621828",
"frequency_reference_population": 0.000016115755,
"hom_count_reference_population": 0,
"allele_count_reference_population": 26,
"gnomad_exomes_af": 0.0000164262,
"gnomad_genomes_af": 0.0000131366,
"gnomad_exomes_ac": 24,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9375097751617432,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.782,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.963,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.26,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.128,
"phylop100way_prediction": "Uncertain_significance",
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000369552.9",
"gene_symbol": "SLC35A1",
"hgnc_id": 11021,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.569T>C",
"hgvs_p": "p.Phe190Ser"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000506888.5",
"gene_symbol": "ENSG00000213204",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1108T>C",
"hgvs_p": null
}
],
"clinvar_disease": "SLC35A1-congenital disorder of glycosylation",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "SLC35A1-congenital disorder of glycosylation",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}