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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: 11-118339201-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=118339201&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 118339201,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_000732.6",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD3D",
"gene_hgnc_id": 1673,
"hgvs_c": "c.477G>A",
"hgvs_p": "p.Gln159Gln",
"transcript": "NM_000732.6",
"protein_id": "NP_000723.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 171,
"cds_start": 477,
"cds_end": null,
"cds_length": 516,
"cdna_start": 575,
"cdna_end": null,
"cdna_length": 701,
"mane_select": "ENST00000300692.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD3D",
"gene_hgnc_id": 1673,
"hgvs_c": "c.477G>A",
"hgvs_p": "p.Gln159Gln",
"transcript": "ENST00000300692.9",
"protein_id": "ENSP00000300692.4",
"transcript_support_level": 1,
"aa_start": 159,
"aa_end": null,
"aa_length": 171,
"cds_start": 477,
"cds_end": null,
"cds_length": 516,
"cdna_start": 575,
"cdna_end": null,
"cdna_length": 701,
"mane_select": "NM_000732.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD3D",
"gene_hgnc_id": 1673,
"hgvs_c": "c.258G>A",
"hgvs_p": "p.Gln86Gln",
"transcript": "ENST00000529594.5",
"protein_id": "ENSP00000437335.1",
"transcript_support_level": 1,
"aa_start": 86,
"aa_end": null,
"aa_length": 98,
"cds_start": 258,
"cds_end": null,
"cds_length": 297,
"cdna_start": 298,
"cdna_end": null,
"cdna_length": 422,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD3D",
"gene_hgnc_id": 1673,
"hgvs_c": "c.345G>A",
"hgvs_p": "p.Gln115Gln",
"transcript": "NM_001040651.2",
"protein_id": "NP_001035741.1",
"transcript_support_level": null,
"aa_start": 115,
"aa_end": null,
"aa_length": 127,
"cds_start": 345,
"cds_end": null,
"cds_length": 384,
"cdna_start": 443,
"cdna_end": null,
"cdna_length": 690,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD3D",
"gene_hgnc_id": 1673,
"hgvs_c": "c.345G>A",
"hgvs_p": "p.Gln115Gln",
"transcript": "ENST00000392884.3",
"protein_id": "ENSP00000376622.2",
"transcript_support_level": 2,
"aa_start": 115,
"aa_end": null,
"aa_length": 127,
"cds_start": 345,
"cds_end": null,
"cds_length": 384,
"cdna_start": 369,
"cdna_end": null,
"cdna_length": 5033,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD3D",
"gene_hgnc_id": 1673,
"hgvs_c": "n.150G>A",
"hgvs_p": null,
"transcript": "ENST00000526561.1",
"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": 257,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD3D",
"gene_hgnc_id": 1673,
"hgvs_c": "n.358G>A",
"hgvs_p": null,
"transcript": "ENST00000534687.5",
"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": 483,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD3D",
"gene_hgnc_id": 1673,
"hgvs_c": "n.1244G>A",
"hgvs_p": null,
"transcript": "ENST00000695666.1",
"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": 1370,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD3D",
"gene_hgnc_id": 1673,
"hgvs_c": "n.762G>A",
"hgvs_p": null,
"transcript": "ENST00000695667.1",
"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": 887,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CD3D",
"gene_hgnc_id": 1673,
"dbsnp": "rs567299359",
"frequency_reference_population": 0.000012391236,
"hom_count_reference_population": 0,
"allele_count_reference_population": 20,
"gnomad_exomes_af": 0.0000116292,
"gnomad_genomes_af": 0.0000197099,
"gnomad_exomes_ac": 17,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.37400001287460327,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "REVEL",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.374,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.44,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.3,
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP6_Moderate,BP7,BS1",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP6_Moderate",
"BP7",
"BS1"
],
"verdict": "Benign",
"transcript": "NM_000732.6",
"gene_symbol": "CD3D",
"hgnc_id": 1673,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.477G>A",
"hgvs_p": "p.Gln159Gln"
}
],
"clinvar_disease": "Immunodeficiency 19",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Immunodeficiency 19",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}