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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: 7-39950689-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=39950689&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 39950689,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_003718.5",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDK13",
"gene_hgnc_id": 1733,
"hgvs_c": "c.48C>T",
"hgvs_p": "p.Ser16Ser",
"transcript": "NM_003718.5",
"protein_id": "NP_003709.3",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 1512,
"cds_start": 48,
"cds_end": null,
"cds_length": 4539,
"cdna_start": 434,
"cdna_end": null,
"cdna_length": 9525,
"mane_select": "ENST00000181839.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDK13",
"gene_hgnc_id": 1733,
"hgvs_c": "c.48C>T",
"hgvs_p": "p.Ser16Ser",
"transcript": "ENST00000181839.10",
"protein_id": "ENSP00000181839.4",
"transcript_support_level": 1,
"aa_start": 16,
"aa_end": null,
"aa_length": 1512,
"cds_start": 48,
"cds_end": null,
"cds_length": 4539,
"cdna_start": 434,
"cdna_end": null,
"cdna_length": 9525,
"mane_select": "NM_003718.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDK13",
"gene_hgnc_id": 1733,
"hgvs_c": "c.48C>T",
"hgvs_p": "p.Ser16Ser",
"transcript": "ENST00000340829.10",
"protein_id": "ENSP00000340557.5",
"transcript_support_level": 1,
"aa_start": 16,
"aa_end": null,
"aa_length": 1452,
"cds_start": 48,
"cds_end": null,
"cds_length": 4359,
"cdna_start": 569,
"cdna_end": null,
"cdna_length": 5455,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDK13",
"gene_hgnc_id": 1733,
"hgvs_c": "c.48C>T",
"hgvs_p": "p.Ser16Ser",
"transcript": "NM_031267.3",
"protein_id": "NP_112557.2",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 1452,
"cds_start": 48,
"cds_end": null,
"cds_length": 4359,
"cdna_start": 330,
"cdna_end": null,
"cdna_length": 6795,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDK13",
"gene_hgnc_id": 1733,
"hgvs_c": "c.48C>T",
"hgvs_p": "p.Ser16Ser",
"transcript": "XM_017012750.3",
"protein_id": "XP_016868239.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 1542,
"cds_start": 48,
"cds_end": null,
"cds_length": 4629,
"cdna_start": 434,
"cdna_end": null,
"cdna_length": 9615,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDK13",
"gene_hgnc_id": 1733,
"hgvs_c": "c.48C>T",
"hgvs_p": "p.Ser16Ser",
"transcript": "XM_017012751.3",
"protein_id": "XP_016868240.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 1482,
"cds_start": 48,
"cds_end": null,
"cds_length": 4449,
"cdna_start": 434,
"cdna_end": null,
"cdna_length": 9435,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDK13",
"gene_hgnc_id": 1733,
"hgvs_c": "c.48C>T",
"hgvs_p": "p.Ser16Ser",
"transcript": "XM_011515597.4",
"protein_id": "XP_011513899.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 905,
"cds_start": 48,
"cds_end": null,
"cds_length": 2718,
"cdna_start": 434,
"cdna_end": null,
"cdna_length": 3966,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CDK13",
"gene_hgnc_id": 1733,
"dbsnp": "rs1011234458",
"frequency_reference_population": 0.0000020987034,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000156582,
"gnomad_genomes_af": 0.00000657151,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5799999833106995,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.58,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.869,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP7",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_003718.5",
"gene_symbol": "CDK13",
"hgnc_id": 1733,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.48C>T",
"hgvs_p": "p.Ser16Ser"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}