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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: 6-53018335-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=53018335&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 53018335,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000676107.1",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CILK1",
"gene_hgnc_id": 21219,
"hgvs_c": "c.658A>G",
"hgvs_p": "p.Lys220Glu",
"transcript": "NM_014920.5",
"protein_id": "NP_055735.1",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 632,
"cds_start": 658,
"cds_end": null,
"cds_length": 1899,
"cdna_start": 1059,
"cdna_end": null,
"cdna_length": 6146,
"mane_select": "ENST00000676107.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CILK1",
"gene_hgnc_id": 21219,
"hgvs_c": "c.658A>G",
"hgvs_p": "p.Lys220Glu",
"transcript": "ENST00000676107.1",
"protein_id": "ENSP00000501692.1",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 632,
"cds_start": 658,
"cds_end": null,
"cds_length": 1899,
"cdna_start": 1059,
"cdna_end": null,
"cdna_length": 6146,
"mane_select": "NM_014920.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CILK1",
"gene_hgnc_id": 21219,
"hgvs_c": "c.658A>G",
"hgvs_p": "p.Lys220Glu",
"transcript": "ENST00000350082.10",
"protein_id": "ENSP00000263043.8",
"transcript_support_level": 1,
"aa_start": 220,
"aa_end": null,
"aa_length": 639,
"cds_start": 658,
"cds_end": null,
"cds_length": 1920,
"cdna_start": 1005,
"cdna_end": null,
"cdna_length": 6137,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CILK1",
"gene_hgnc_id": 21219,
"hgvs_c": "c.658A>G",
"hgvs_p": "p.Lys220Glu",
"transcript": "NM_001375397.1",
"protein_id": "NP_001362326.1",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 639,
"cds_start": 658,
"cds_end": null,
"cds_length": 1920,
"cdna_start": 1059,
"cdna_end": null,
"cdna_length": 6167,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CILK1",
"gene_hgnc_id": 21219,
"hgvs_c": "c.658A>G",
"hgvs_p": "p.Lys220Glu",
"transcript": "NM_001375398.1",
"protein_id": "NP_001362327.1",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 632,
"cds_start": 658,
"cds_end": null,
"cds_length": 1899,
"cdna_start": 1843,
"cdna_end": null,
"cdna_length": 6930,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CILK1",
"gene_hgnc_id": 21219,
"hgvs_c": "c.658A>G",
"hgvs_p": "p.Lys220Glu",
"transcript": "NM_001375399.1",
"protein_id": "NP_001362328.1",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 632,
"cds_start": 658,
"cds_end": null,
"cds_length": 1899,
"cdna_start": 1313,
"cdna_end": null,
"cdna_length": 6400,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CILK1",
"gene_hgnc_id": 21219,
"hgvs_c": "c.658A>G",
"hgvs_p": "p.Lys220Glu",
"transcript": "NM_001375400.1",
"protein_id": "NP_001362329.1",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 632,
"cds_start": 658,
"cds_end": null,
"cds_length": 1899,
"cdna_start": 1183,
"cdna_end": null,
"cdna_length": 6270,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CILK1",
"gene_hgnc_id": 21219,
"hgvs_c": "c.658A>G",
"hgvs_p": "p.Lys220Glu",
"transcript": "NM_001375401.1",
"protein_id": "NP_001362330.1",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 632,
"cds_start": 658,
"cds_end": null,
"cds_length": 1899,
"cdna_start": 1189,
"cdna_end": null,
"cdna_length": 6276,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CILK1",
"gene_hgnc_id": 21219,
"hgvs_c": "c.658A>G",
"hgvs_p": "p.Lys220Glu",
"transcript": "NM_001375402.1",
"protein_id": "NP_001362331.1",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 632,
"cds_start": 658,
"cds_end": null,
"cds_length": 1899,
"cdna_start": 1233,
"cdna_end": null,
"cdna_length": 6320,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CILK1",
"gene_hgnc_id": 21219,
"hgvs_c": "c.658A>G",
"hgvs_p": "p.Lys220Glu",
"transcript": "NM_016513.5",
"protein_id": "NP_057597.2",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 632,
"cds_start": 658,
"cds_end": null,
"cds_length": 1899,
"cdna_start": 1170,
"cdna_end": null,
"cdna_length": 6257,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CILK1",
"gene_hgnc_id": 21219,
"hgvs_c": "c.658A>G",
"hgvs_p": "p.Lys220Glu",
"transcript": "ENST00000356971.3",
"protein_id": "ENSP00000349458.3",
"transcript_support_level": 2,
"aa_start": 220,
"aa_end": null,
"aa_length": 632,
"cds_start": 658,
"cds_end": null,
"cds_length": 1899,
"cdna_start": 1148,
"cdna_end": null,
"cdna_length": 6227,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CILK1",
"gene_hgnc_id": 21219,
"hgvs_c": "n.1059A>G",
"hgvs_p": null,
"transcript": "NR_164684.1",
"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": 6257,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CILK1",
"gene_hgnc_id": 21219,
"dbsnp": "rs1554169267",
"frequency_reference_population": 6.840759e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84076e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4840538501739502,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.25,
"revel_prediction": "Benign",
"alphamissense_score": 0.2865,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.07,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 8.007,
"phylop100way_prediction": "Pathogenic",
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000676107.1",
"gene_symbol": "CILK1",
"hgnc_id": 21219,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.658A>G",
"hgvs_p": "p.Lys220Glu"
}
],
"clinvar_disease": " 10, juvenile myoclonic, susceptibility to,Epilepsy",
"clinvar_classification": "risk factor",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Epilepsy, juvenile myoclonic, susceptibility to, 10",
"pathogenicity_classification_combined": "risk factor",
"custom_annotations": null
}
],
"message": null
}