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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: 4-55981340-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=55981340&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 55981340,
"ref": "A",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "ENST00000257287.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "c.1740A>G",
"hgvs_p": "p.Arg580Arg",
"transcript": "NM_025009.5",
"protein_id": "NP_079285.2",
"transcript_support_level": null,
"aa_start": 580,
"aa_end": null,
"aa_length": 1140,
"cds_start": 1740,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 1900,
"cdna_end": null,
"cdna_length": 5596,
"mane_select": "ENST00000257287.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "c.1740A>G",
"hgvs_p": "p.Arg580Arg",
"transcript": "ENST00000257287.5",
"protein_id": "ENSP00000257287.3",
"transcript_support_level": 1,
"aa_start": 580,
"aa_end": null,
"aa_length": 1140,
"cds_start": 1740,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 1900,
"cdna_end": null,
"cdna_length": 5596,
"mane_select": "NM_025009.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "n.1690A>G",
"hgvs_p": null,
"transcript": "ENST00000506202.1",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5129,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "c.1707A>G",
"hgvs_p": "p.Arg569Arg",
"transcript": "XM_006714055.4",
"protein_id": "XP_006714118.1",
"transcript_support_level": null,
"aa_start": 569,
"aa_end": null,
"aa_length": 1129,
"cds_start": 1707,
"cds_end": null,
"cds_length": 3390,
"cdna_start": 1867,
"cdna_end": null,
"cdna_length": 5563,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "c.669A>G",
"hgvs_p": "p.Arg223Arg",
"transcript": "XM_005265788.5",
"protein_id": "XP_005265845.1",
"transcript_support_level": null,
"aa_start": 223,
"aa_end": null,
"aa_length": 783,
"cds_start": 669,
"cds_end": null,
"cds_length": 2352,
"cdna_start": 780,
"cdna_end": null,
"cdna_length": 4476,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "c.210A>G",
"hgvs_p": "p.Arg70Arg",
"transcript": "XM_011534412.2",
"protein_id": "XP_011532714.1",
"transcript_support_level": null,
"aa_start": 70,
"aa_end": null,
"aa_length": 630,
"cds_start": 210,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 356,
"cdna_end": null,
"cdna_length": 4052,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000299857",
"gene_hgnc_id": null,
"hgvs_c": "n.108-5258T>C",
"hgvs_p": null,
"transcript": "ENST00000766957.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 402,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"dbsnp": "rs59759676",
"frequency_reference_population": 0.000582675,
"hom_count_reference_population": 1,
"allele_count_reference_population": 925,
"gnomad_exomes_af": 0.000494007,
"gnomad_genomes_af": 0.00141822,
"gnomad_exomes_ac": 709,
"gnomad_genomes_ac": 216,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5099999904632568,
"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": -0.51,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.935,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BP7,BS1",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BP7",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000257287.5",
"gene_symbol": "CEP135",
"hgnc_id": 29086,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1740A>G",
"hgvs_p": "p.Arg580Arg"
},
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000766957.1",
"gene_symbol": "ENSG00000299857",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.108-5258T>C",
"hgvs_p": null
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 B:1",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}