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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: 2-171522589-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=171522589&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 171522589,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_024843.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBRD1",
"gene_hgnc_id": 20797,
"hgvs_c": "c.44C>T",
"hgvs_p": "p.Ser15Leu",
"transcript": "NM_024843.4",
"protein_id": "NP_079119.3",
"transcript_support_level": null,
"aa_start": 15,
"aa_end": null,
"aa_length": 286,
"cds_start": 44,
"cds_end": null,
"cds_length": 861,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000321348.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024843.4"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBRD1",
"gene_hgnc_id": 20797,
"hgvs_c": "c.44C>T",
"hgvs_p": "p.Ser15Leu",
"transcript": "ENST00000321348.9",
"protein_id": "ENSP00000319141.4",
"transcript_support_level": 1,
"aa_start": 15,
"aa_end": null,
"aa_length": 286,
"cds_start": 44,
"cds_end": null,
"cds_length": 861,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_024843.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000321348.9"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBRD1",
"gene_hgnc_id": 20797,
"hgvs_c": "c.44C>T",
"hgvs_p": "p.Ser15Leu",
"transcript": "ENST00000375252.3",
"protein_id": "ENSP00000364401.3",
"transcript_support_level": 1,
"aa_start": 15,
"aa_end": null,
"aa_length": 157,
"cds_start": 44,
"cds_end": null,
"cds_length": 474,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375252.3"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBRD1",
"gene_hgnc_id": 20797,
"hgvs_c": "c.44C>T",
"hgvs_p": "p.Ser15Leu",
"transcript": "ENST00000858692.1",
"protein_id": "ENSP00000528751.1",
"transcript_support_level": null,
"aa_start": 15,
"aa_end": null,
"aa_length": 285,
"cds_start": 44,
"cds_end": null,
"cds_length": 858,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858692.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBRD1",
"gene_hgnc_id": 20797,
"hgvs_c": "c.44C>T",
"hgvs_p": "p.Ser15Leu",
"transcript": "NM_001127383.2",
"protein_id": "NP_001120855.1",
"transcript_support_level": null,
"aa_start": 15,
"aa_end": null,
"aa_length": 157,
"cds_start": 44,
"cds_end": null,
"cds_length": 474,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001127383.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CYBRD1",
"gene_hgnc_id": 20797,
"hgvs_c": "c.19+298C>T",
"hgvs_p": null,
"transcript": "NM_001256909.2",
"protein_id": "NP_001243838.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 228,
"cds_start": null,
"cds_end": null,
"cds_length": 687,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001256909.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CYBRD1",
"gene_hgnc_id": 20797,
"hgvs_c": "c.19+298C>T",
"hgvs_p": null,
"transcript": "ENST00000409484.5",
"protein_id": "ENSP00000386739.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 228,
"cds_start": null,
"cds_end": null,
"cds_length": 687,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409484.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBRD1",
"gene_hgnc_id": 20797,
"hgvs_c": "n.242C>T",
"hgvs_p": null,
"transcript": "ENST00000468308.1",
"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": "ENST00000468308.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBRD1",
"gene_hgnc_id": 20797,
"hgvs_c": "n.80C>T",
"hgvs_p": null,
"transcript": "ENST00000474182.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000474182.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYBRD1",
"gene_hgnc_id": 20797,
"hgvs_c": "n.79C>T",
"hgvs_p": null,
"transcript": "ENST00000494587.1",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000494587.1"
}
],
"gene_symbol": "CYBRD1",
"gene_hgnc_id": 20797,
"dbsnp": "rs146713767",
"frequency_reference_population": 0.0015283081,
"hom_count_reference_population": 4,
"allele_count_reference_population": 2463,
"gnomad_exomes_af": 0.00158843,
"gnomad_genomes_af": 0.000952156,
"gnomad_exomes_ac": 2318,
"gnomad_genomes_ac": 145,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.00937393307685852,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.083,
"revel_prediction": "Benign",
"alphamissense_score": 0.1456,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.34,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.015,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_024843.4",
"gene_symbol": "CYBRD1",
"hgnc_id": 20797,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.44C>T",
"hgvs_p": "p.Ser15Leu"
}
],
"clinvar_disease": "CYBRD1-related disorder",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "CYBRD1-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}