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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: 5-157248975-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=157248975&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 157248975,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_005546.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITK",
"gene_hgnc_id": 6171,
"hgvs_c": "c.1759G>T",
"hgvs_p": "p.Val587Phe",
"transcript": "NM_005546.4",
"protein_id": "NP_005537.3",
"transcript_support_level": null,
"aa_start": 587,
"aa_end": null,
"aa_length": 620,
"cds_start": 1759,
"cds_end": null,
"cds_length": 1863,
"cdna_start": 1897,
"cdna_end": null,
"cdna_length": 4508,
"mane_select": "ENST00000422843.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005546.4"
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITK",
"gene_hgnc_id": 6171,
"hgvs_c": "c.1759G>T",
"hgvs_p": "p.Val587Phe",
"transcript": "ENST00000422843.8",
"protein_id": "ENSP00000398655.4",
"transcript_support_level": 1,
"aa_start": 587,
"aa_end": null,
"aa_length": 620,
"cds_start": 1759,
"cds_end": null,
"cds_length": 1863,
"cdna_start": 1897,
"cdna_end": null,
"cdna_length": 4508,
"mane_select": "NM_005546.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000422843.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITK",
"gene_hgnc_id": 6171,
"hgvs_c": "n.764G>T",
"hgvs_p": null,
"transcript": "ENST00000519749.1",
"protein_id": null,
"transcript_support_level": 1,
"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": 3375,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000519749.1"
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITK",
"gene_hgnc_id": 6171,
"hgvs_c": "c.1735G>T",
"hgvs_p": "p.Val579Phe",
"transcript": "ENST00000862614.1",
"protein_id": "ENSP00000532673.1",
"transcript_support_level": null,
"aa_start": 579,
"aa_end": null,
"aa_length": 612,
"cds_start": 1735,
"cds_end": null,
"cds_length": 1839,
"cdna_start": 1891,
"cdna_end": null,
"cdna_length": 4502,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862614.1"
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITK",
"gene_hgnc_id": 6171,
"hgvs_c": "c.1732G>T",
"hgvs_p": "p.Val578Phe",
"transcript": "ENST00000862615.1",
"protein_id": "ENSP00000532674.1",
"transcript_support_level": null,
"aa_start": 578,
"aa_end": null,
"aa_length": 611,
"cds_start": 1732,
"cds_end": null,
"cds_length": 1836,
"cdna_start": 1832,
"cdna_end": null,
"cdna_length": 4358,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862615.1"
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITK",
"gene_hgnc_id": 6171,
"hgvs_c": "c.1654G>T",
"hgvs_p": "p.Val552Phe",
"transcript": "ENST00000862616.1",
"protein_id": "ENSP00000532675.1",
"transcript_support_level": null,
"aa_start": 552,
"aa_end": null,
"aa_length": 585,
"cds_start": 1654,
"cds_end": null,
"cds_length": 1758,
"cdna_start": 1659,
"cdna_end": null,
"cdna_length": 4256,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862616.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITK",
"gene_hgnc_id": 6171,
"hgvs_c": "n.3344G>T",
"hgvs_p": null,
"transcript": "ENST00000519402.5",
"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": 5869,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000519402.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITK",
"gene_hgnc_id": 6171,
"hgvs_c": "n.*536G>T",
"hgvs_p": null,
"transcript": "ENST00000696962.1",
"protein_id": "ENSP00000513001.1",
"transcript_support_level": null,
"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": 4256,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000696962.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITK",
"gene_hgnc_id": 6171,
"hgvs_c": "n.*536G>T",
"hgvs_p": null,
"transcript": "ENST00000696962.1",
"protein_id": "ENSP00000513001.1",
"transcript_support_level": null,
"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": 4256,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000696962.1"
}
],
"gene_symbol": "ITK",
"gene_hgnc_id": 6171,
"dbsnp": "rs56005928",
"frequency_reference_population": 6.8417705e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84177e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9351084232330322,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.523,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.4998,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.18,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.017,
"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": 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": "NM_005546.4",
"gene_symbol": "ITK",
"hgnc_id": 6171,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1759G>T",
"hgvs_p": "p.Val587Phe"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}