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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: 4-56019496-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=56019496&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 5,
"criteria": [
"PM2",
"BP4_Strong",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "CEP135",
"hgnc_id": 29086,
"hgvs_c": "c.3156C>T",
"hgvs_p": "p.His1052His",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -3,
"transcript": "NM_025009.5",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP7",
"acmg_score": -3,
"allele_count_reference_population": 21,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.64,
"chr": "4",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.6399999856948853,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1140,
"aa_ref": "H",
"aa_start": 1052,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5596,
"cdna_start": 3316,
"cds_end": null,
"cds_length": 3423,
"cds_start": 3156,
"consequences": [
"synonymous_variant"
],
"exon_count": 26,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "NM_025009.5",
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"hgvs_c": "c.3156C>T",
"hgvs_p": "p.His1052His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000257287.5",
"protein_coding": true,
"protein_id": "NP_079285.2",
"strand": true,
"transcript": "NM_025009.5",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1140,
"aa_ref": "H",
"aa_start": 1052,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5596,
"cdna_start": 3316,
"cds_end": null,
"cds_length": 3423,
"cds_start": 3156,
"consequences": [
"synonymous_variant"
],
"exon_count": 26,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "ENST00000257287.5",
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"hgvs_c": "c.3156C>T",
"hgvs_p": "p.His1052His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_025009.5",
"protein_coding": true,
"protein_id": "ENSP00000257287.3",
"strand": true,
"transcript": "ENST00000257287.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 5129,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 19,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000506202.1",
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"hgvs_c": "n.3106C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000506202.1",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1191,
"aa_ref": "H",
"aa_start": 1103,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5781,
"cdna_start": 3501,
"cds_end": null,
"cds_length": 3576,
"cds_start": 3309,
"consequences": [
"synonymous_variant"
],
"exon_count": 27,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000916105.1",
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"hgvs_c": "c.3309C>T",
"hgvs_p": "p.His1103His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586164.1",
"strand": true,
"transcript": "ENST00000916105.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1129,
"aa_ref": "H",
"aa_start": 1041,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5651,
"cdna_start": 3376,
"cds_end": null,
"cds_length": 3390,
"cds_start": 3123,
"consequences": [
"synonymous_variant"
],
"exon_count": 26,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "ENST00000916104.1",
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"hgvs_c": "c.3123C>T",
"hgvs_p": "p.His1041His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586163.1",
"strand": true,
"transcript": "ENST00000916104.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1118,
"aa_ref": "H",
"aa_start": 1030,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5405,
"cdna_start": 3376,
"cds_end": null,
"cds_length": 3357,
"cds_start": 3090,
"consequences": [
"synonymous_variant"
],
"exon_count": 25,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000916107.1",
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"hgvs_c": "c.3090C>T",
"hgvs_p": "p.His1030His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586166.1",
"strand": true,
"transcript": "ENST00000916107.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1097,
"aa_ref": "H",
"aa_start": 1009,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5494,
"cdna_start": 3215,
"cds_end": null,
"cds_length": 3294,
"cds_start": 3027,
"consequences": [
"synonymous_variant"
],
"exon_count": 25,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000916106.1",
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"hgvs_c": "c.3027C>T",
"hgvs_p": "p.His1009His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586165.1",
"strand": true,
"transcript": "ENST00000916106.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1129,
"aa_ref": "H",
"aa_start": 1041,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5563,
"cdna_start": 3283,
"cds_end": null,
"cds_length": 3390,
"cds_start": 3123,
"consequences": [
"synonymous_variant"
],
"exon_count": 26,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "XM_006714055.4",
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"hgvs_c": "c.3123C>T",
"hgvs_p": "p.His1041His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006714118.1",
"strand": true,
"transcript": "XM_006714055.4",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 783,
"aa_ref": "H",
"aa_start": 695,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4476,
"cdna_start": 2196,
"cds_end": null,
"cds_length": 2352,
"cds_start": 2085,
"consequences": [
"synonymous_variant"
],
"exon_count": 19,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "XM_005265788.5",
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"hgvs_c": "c.2085C>T",
"hgvs_p": "p.His695His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005265845.1",
"strand": true,
"transcript": "XM_005265788.5",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 630,
"aa_ref": "H",
"aa_start": 542,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4052,
"cdna_start": 1772,
"cds_end": null,
"cds_length": 1893,
"cds_start": 1626,
"consequences": [
"synonymous_variant"
],
"exon_count": 16,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "XM_011534412.2",
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"hgvs_c": "c.1626C>T",
"hgvs_p": "p.His542His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011532714.1",
"strand": true,
"transcript": "XM_011534412.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3285,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000706801.1",
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"hgvs_c": "n.1221C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000706801.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs376309359",
"effect": "synonymous_variant",
"frequency_reference_population": 0.000013011959,
"gene_hgnc_id": 29086,
"gene_symbol": "CEP135",
"gnomad_exomes_ac": 19,
"gnomad_exomes_af": 0.0000129984,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131418,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": -2.377,
"pos": 56019496,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_025009.5"
}
]
}