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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: 4-56011440-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=56011440&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 56011440,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_025009.5",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "c.2534T>C",
"hgvs_p": "p.Val845Ala",
"transcript": "NM_025009.5",
"protein_id": "NP_079285.2",
"transcript_support_level": null,
"aa_start": 845,
"aa_end": null,
"aa_length": 1140,
"cds_start": 2534,
"cds_end": null,
"cds_length": 3423,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000257287.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_025009.5"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "c.2534T>C",
"hgvs_p": "p.Val845Ala",
"transcript": "ENST00000257287.5",
"protein_id": "ENSP00000257287.3",
"transcript_support_level": 1,
"aa_start": 845,
"aa_end": null,
"aa_length": 1140,
"cds_start": 2534,
"cds_end": null,
"cds_length": 3423,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_025009.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000257287.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "n.2484T>C",
"hgvs_p": null,
"transcript": "ENST00000506202.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000506202.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "c.2534T>C",
"hgvs_p": "p.Val845Ala",
"transcript": "ENST00000916105.1",
"protein_id": "ENSP00000586164.1",
"transcript_support_level": null,
"aa_start": 845,
"aa_end": null,
"aa_length": 1191,
"cds_start": 2534,
"cds_end": null,
"cds_length": 3576,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916105.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "c.2501T>C",
"hgvs_p": "p.Val834Ala",
"transcript": "ENST00000916104.1",
"protein_id": "ENSP00000586163.1",
"transcript_support_level": null,
"aa_start": 834,
"aa_end": null,
"aa_length": 1129,
"cds_start": 2501,
"cds_end": null,
"cds_length": 3390,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916104.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "c.2468T>C",
"hgvs_p": "p.Val823Ala",
"transcript": "ENST00000916107.1",
"protein_id": "ENSP00000586166.1",
"transcript_support_level": null,
"aa_start": 823,
"aa_end": null,
"aa_length": 1118,
"cds_start": 2468,
"cds_end": null,
"cds_length": 3357,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916107.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "c.2405T>C",
"hgvs_p": "p.Val802Ala",
"transcript": "ENST00000916106.1",
"protein_id": "ENSP00000586165.1",
"transcript_support_level": null,
"aa_start": 802,
"aa_end": null,
"aa_length": 1097,
"cds_start": 2405,
"cds_end": null,
"cds_length": 3294,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916106.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "c.2501T>C",
"hgvs_p": "p.Val834Ala",
"transcript": "XM_006714055.4",
"protein_id": "XP_006714118.1",
"transcript_support_level": null,
"aa_start": 834,
"aa_end": null,
"aa_length": 1129,
"cds_start": 2501,
"cds_end": null,
"cds_length": 3390,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006714055.4"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "c.1463T>C",
"hgvs_p": "p.Val488Ala",
"transcript": "XM_005265788.5",
"protein_id": "XP_005265845.1",
"transcript_support_level": null,
"aa_start": 488,
"aa_end": null,
"aa_length": 783,
"cds_start": 1463,
"cds_end": null,
"cds_length": 2352,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005265788.5"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "c.1004T>C",
"hgvs_p": "p.Val335Ala",
"transcript": "XM_011534412.2",
"protein_id": "XP_011532714.1",
"transcript_support_level": null,
"aa_start": 335,
"aa_end": null,
"aa_length": 630,
"cds_start": 1004,
"cds_end": null,
"cds_length": 1893,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011534412.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"hgvs_c": "n.599T>C",
"hgvs_p": null,
"transcript": "ENST00000706801.1",
"protein_id": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000706801.1"
}
],
"gene_symbol": "CEP135",
"gene_hgnc_id": 29086,
"dbsnp": "rs141330867",
"frequency_reference_population": 0.000060776172,
"hom_count_reference_population": 1,
"allele_count_reference_population": 98,
"gnomad_exomes_af": 0.000054786,
"gnomad_genomes_af": 0.00011823,
"gnomad_exomes_ac": 80,
"gnomad_genomes_ac": 18,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.02574220299720764,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.083,
"revel_prediction": "Benign",
"alphamissense_score": 0.1715,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.598,
"phylop100way_prediction": "Uncertain_significance",
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP6",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "NM_025009.5",
"gene_symbol": "CEP135",
"hgnc_id": 29086,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2534T>C",
"hgvs_p": "p.Val845Ala"
}
],
"clinvar_disease": " autosomal recessive, primary,Inborn genetic diseases,Microcephaly 8,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:1",
"phenotype_combined": "not specified|not provided|Microcephaly 8, primary, autosomal recessive|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}