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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: 19-541539-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=541539&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 541539,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004359.2",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDC34",
"gene_hgnc_id": 1734,
"hgvs_c": "c.698C>T",
"hgvs_p": "p.Thr233Met",
"transcript": "NM_004359.2",
"protein_id": "NP_004350.1",
"transcript_support_level": null,
"aa_start": 233,
"aa_end": null,
"aa_length": 236,
"cds_start": 698,
"cds_end": null,
"cds_length": 711,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000215574.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004359.2"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDC34",
"gene_hgnc_id": 1734,
"hgvs_c": "c.698C>T",
"hgvs_p": "p.Thr233Met",
"transcript": "ENST00000215574.9",
"protein_id": "ENSP00000215574.2",
"transcript_support_level": 1,
"aa_start": 233,
"aa_end": null,
"aa_length": 236,
"cds_start": 698,
"cds_end": null,
"cds_length": 711,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004359.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000215574.9"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDC34",
"gene_hgnc_id": 1734,
"hgvs_c": "c.806C>T",
"hgvs_p": "p.Thr269Met",
"transcript": "ENST00000874791.1",
"protein_id": "ENSP00000544850.1",
"transcript_support_level": null,
"aa_start": 269,
"aa_end": null,
"aa_length": 272,
"cds_start": 806,
"cds_end": null,
"cds_length": 819,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874791.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDC34",
"gene_hgnc_id": 1734,
"hgvs_c": "c.611C>T",
"hgvs_p": "p.Thr204Met",
"transcript": "ENST00000874793.1",
"protein_id": "ENSP00000544852.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 207,
"cds_start": 611,
"cds_end": null,
"cds_length": 624,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874793.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDC34",
"gene_hgnc_id": 1734,
"hgvs_c": "c.563C>T",
"hgvs_p": "p.Thr188Met",
"transcript": "ENST00000874792.1",
"protein_id": "ENSP00000544851.1",
"transcript_support_level": null,
"aa_start": 188,
"aa_end": null,
"aa_length": 191,
"cds_start": 563,
"cds_end": null,
"cds_length": 576,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874792.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDC34",
"gene_hgnc_id": 1734,
"hgvs_c": "c.311C>T",
"hgvs_p": "p.Thr104Met",
"transcript": "ENST00000607527.5",
"protein_id": "ENSP00000476107.2",
"transcript_support_level": 5,
"aa_start": 104,
"aa_end": null,
"aa_length": 107,
"cds_start": 311,
"cds_end": null,
"cds_length": 324,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000607527.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDC34",
"gene_hgnc_id": 1734,
"hgvs_c": "c.*154C>T",
"hgvs_p": null,
"transcript": "ENST00000586283.6",
"protein_id": "ENSP00000475282.3",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 145,
"cds_start": null,
"cds_end": null,
"cds_length": 438,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000586283.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDC34",
"gene_hgnc_id": 1734,
"hgvs_c": "c.*154C>T",
"hgvs_p": null,
"transcript": "ENST00000606065.3",
"protein_id": "ENSP00000475610.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 119,
"cds_start": null,
"cds_end": null,
"cds_length": 360,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000606065.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDC34",
"gene_hgnc_id": 1734,
"hgvs_c": "c.*154C>T",
"hgvs_p": null,
"transcript": "XM_006722952.3",
"protein_id": "XP_006723015.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 179,
"cds_start": null,
"cds_end": null,
"cds_length": 540,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006722952.3"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDC34",
"gene_hgnc_id": 1734,
"hgvs_c": "n.237C>T",
"hgvs_p": null,
"transcript": "ENST00000593036.4",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000593036.4"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDC34",
"gene_hgnc_id": 1734,
"hgvs_c": "n.396C>T",
"hgvs_p": null,
"transcript": "ENST00000606400.3",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000606400.3"
}
],
"gene_symbol": "CDC34",
"gene_hgnc_id": 1734,
"dbsnp": "rs750335335",
"frequency_reference_population": 0.000009030713,
"hom_count_reference_population": 0,
"allele_count_reference_population": 13,
"gnomad_exomes_af": 0.00000903071,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 13,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.11778244376182556,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.204,
"revel_prediction": "Benign",
"alphamissense_score": 0.1038,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.56,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.243,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 2,
"pathogenic_score": 4,
"criteria": [
"PM1",
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_004359.2",
"gene_symbol": "CDC34",
"hgnc_id": 1734,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.698C>T",
"hgvs_p": "p.Thr233Met"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}