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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: 19-48750557-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=48750557&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 48750557,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_000148.4",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FUT1",
"gene_hgnc_id": 4012,
"hgvs_c": "c.725T>G",
"hgvs_p": "p.Leu242Arg",
"transcript": "NM_001384359.1",
"protein_id": "NP_001371288.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 365,
"cds_start": 725,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000645652.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001384359.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FUT1",
"gene_hgnc_id": 4012,
"hgvs_c": "c.725T>G",
"hgvs_p": "p.Leu242Arg",
"transcript": "ENST00000645652.2",
"protein_id": "ENSP00000494643.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 365,
"cds_start": 725,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001384359.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000645652.2"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FUT1",
"gene_hgnc_id": 4012,
"hgvs_c": "c.725T>G",
"hgvs_p": "p.Leu242Arg",
"transcript": "NM_000148.4",
"protein_id": "NP_000139.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 365,
"cds_start": 725,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000148.4"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FUT1",
"gene_hgnc_id": 4012,
"hgvs_c": "c.725T>G",
"hgvs_p": "p.Leu242Arg",
"transcript": "NM_001329877.1",
"protein_id": "NP_001316806.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 365,
"cds_start": 725,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001329877.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FUT1",
"gene_hgnc_id": 4012,
"hgvs_c": "c.725T>G",
"hgvs_p": "p.Leu242Arg",
"transcript": "ENST00000927212.1",
"protein_id": "ENSP00000597271.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 365,
"cds_start": 725,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000927212.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FUT1",
"gene_hgnc_id": 4012,
"hgvs_c": "c.725T>G",
"hgvs_p": "p.Leu242Arg",
"transcript": "ENST00000927213.1",
"protein_id": "ENSP00000597272.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 365,
"cds_start": 725,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000927213.1"
}
],
"gene_symbol": "FUT1",
"gene_hgnc_id": 4012,
"dbsnp": "rs28934588",
"frequency_reference_population": 0.00010852659,
"hom_count_reference_population": 0,
"allele_count_reference_population": 175,
"gnomad_exomes_af": 0.00011437,
"gnomad_genomes_af": 0.0000525176,
"gnomad_exomes_ac": 167,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7431108951568604,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.884,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8411,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.53,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.046,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP5",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 0,
"pathogenic_score": 1,
"criteria": [
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000148.4",
"gene_symbol": "FUT1",
"hgnc_id": 4012,
"effects": [
"missense_variant"
],
"inheritance_mode": "BG",
"hgvs_c": "c.725T>G",
"hgvs_p": "p.Leu242Arg"
}
],
"clinvar_disease": " DIGENIC,BOMBAY PHENOTYPE,Bombay phenotype",
"clinvar_classification": " Affects,Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "BOMBAY PHENOTYPE, DIGENIC|Bombay phenotype",
"pathogenicity_classification_combined": "Pathogenic; Affects",
"custom_annotations": null
}
],
"message": null
}