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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: 19-48750399-CAA-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=48750399&ref=CAA&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1_Strong",
"PP5"
],
"effects": [
"frameshift_variant"
],
"gene_symbol": "FUT1",
"hgnc_id": 4012,
"hgvs_c": "c.881_882delTT",
"hgvs_p": "p.Phe294fs",
"inheritance_mode": "BG",
"pathogenic_score": 5,
"score": 5,
"transcript": "NM_000148.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PVS1_Strong,PP5",
"acmg_score": 5,
"allele_count_reference_population": 51,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "19",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "FUT1-related disorder",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 365,
"aa_ref": "F",
"aa_start": 294,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3425,
"cdna_start": 1036,
"cds_end": null,
"cds_length": 1098,
"cds_start": 881,
"consequences": [
"frameshift_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001384359.1",
"gene_hgnc_id": 4012,
"gene_symbol": "FUT1",
"hgvs_c": "c.881_882delTT",
"hgvs_p": "p.Phe294fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000645652.2",
"protein_coding": true,
"protein_id": "NP_001371288.1",
"strand": false,
"transcript": "NM_001384359.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 365,
"aa_ref": "F",
"aa_start": 294,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3425,
"cdna_start": 1036,
"cds_end": null,
"cds_length": 1098,
"cds_start": 881,
"consequences": [
"frameshift_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000645652.2",
"gene_hgnc_id": 4012,
"gene_symbol": "FUT1",
"hgvs_c": "c.881_882delTT",
"hgvs_p": "p.Phe294fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001384359.1",
"protein_coding": true,
"protein_id": "ENSP00000494643.1",
"strand": false,
"transcript": "ENST00000645652.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 365,
"aa_ref": "F",
"aa_start": 294,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4214,
"cdna_start": 1825,
"cds_end": null,
"cds_length": 1098,
"cds_start": 881,
"consequences": [
"frameshift_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_000148.4",
"gene_hgnc_id": 4012,
"gene_symbol": "FUT1",
"hgvs_c": "c.881_882delTT",
"hgvs_p": "p.Phe294fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_000139.1",
"strand": false,
"transcript": "NM_000148.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 365,
"aa_ref": "F",
"aa_start": 294,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3992,
"cdna_start": 1603,
"cds_end": null,
"cds_length": 1098,
"cds_start": 881,
"consequences": [
"frameshift_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001329877.1",
"gene_hgnc_id": 4012,
"gene_symbol": "FUT1",
"hgvs_c": "c.881_882delTT",
"hgvs_p": "p.Phe294fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001316806.1",
"strand": false,
"transcript": "NM_001329877.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 365,
"aa_ref": "F",
"aa_start": 294,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3367,
"cdna_start": 978,
"cds_end": null,
"cds_length": 1098,
"cds_start": 881,
"consequences": [
"frameshift_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000927212.1",
"gene_hgnc_id": 4012,
"gene_symbol": "FUT1",
"hgvs_c": "c.881_882delTT",
"hgvs_p": "p.Phe294fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000597271.1",
"strand": false,
"transcript": "ENST00000927212.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 365,
"aa_ref": "F",
"aa_start": 294,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3387,
"cdna_start": 998,
"cds_end": null,
"cds_length": 1098,
"cds_start": 881,
"consequences": [
"frameshift_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000927213.1",
"gene_hgnc_id": 4012,
"gene_symbol": "FUT1",
"hgvs_c": "c.881_882delTT",
"hgvs_p": "p.Phe294fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000597272.1",
"strand": false,
"transcript": "ENST00000927213.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs777455020",
"effect": "frameshift_variant",
"frequency_reference_population": 0.000031596475,
"gene_hgnc_id": 4012,
"gene_symbol": "FUT1",
"gnomad_exomes_ac": 39,
"gnomad_exomes_af": 0.0000266778,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 12,
"gnomad_genomes_af": 0.0000788353,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "FUT1-related disorder",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.641,
"pos": 48750399,
"ref": "CAA",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000148.4"
}
]
}