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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: X-18613214-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=18613214&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 18613214,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000623535.2",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"hgvs_c": "c.2215C>T",
"hgvs_p": "p.Leu739Leu",
"transcript": "NM_001323289.2",
"protein_id": "NP_001310218.1",
"transcript_support_level": null,
"aa_start": 739,
"aa_end": null,
"aa_length": 960,
"cds_start": 2215,
"cds_end": null,
"cds_length": 2883,
"cdna_start": 2465,
"cdna_end": null,
"cdna_length": 14572,
"mane_select": "ENST00000623535.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"hgvs_c": "c.2215C>T",
"hgvs_p": "p.Leu739Leu",
"transcript": "ENST00000623535.2",
"protein_id": "ENSP00000485244.1",
"transcript_support_level": 1,
"aa_start": 739,
"aa_end": null,
"aa_length": 960,
"cds_start": 2215,
"cds_end": null,
"cds_length": 2883,
"cdna_start": 2465,
"cdna_end": null,
"cdna_length": 14572,
"mane_select": "NM_001323289.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"hgvs_c": "c.2215C>T",
"hgvs_p": "p.Leu739Leu",
"transcript": "ENST00000379989.6",
"protein_id": "ENSP00000369325.3",
"transcript_support_level": 1,
"aa_start": 739,
"aa_end": null,
"aa_length": 1030,
"cds_start": 2215,
"cds_end": null,
"cds_length": 3093,
"cdna_start": 2500,
"cdna_end": null,
"cdna_length": 3463,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"hgvs_c": "c.2215C>T",
"hgvs_p": "p.Leu739Leu",
"transcript": "ENST00000379996.7",
"protein_id": "ENSP00000369332.3",
"transcript_support_level": 1,
"aa_start": 739,
"aa_end": null,
"aa_length": 1030,
"cds_start": 2215,
"cds_end": null,
"cds_length": 3093,
"cdna_start": 2490,
"cdna_end": null,
"cdna_length": 3449,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"hgvs_c": "c.2215C>T",
"hgvs_p": "p.Leu739Leu",
"transcript": "NM_001037343.2",
"protein_id": "NP_001032420.1",
"transcript_support_level": null,
"aa_start": 739,
"aa_end": null,
"aa_length": 1030,
"cds_start": 2215,
"cds_end": null,
"cds_length": 3093,
"cdna_start": 2464,
"cdna_end": null,
"cdna_length": 3427,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"hgvs_c": "c.2215C>T",
"hgvs_p": "p.Leu739Leu",
"transcript": "NM_003159.3",
"protein_id": "NP_003150.1",
"transcript_support_level": null,
"aa_start": 739,
"aa_end": null,
"aa_length": 1030,
"cds_start": 2215,
"cds_end": null,
"cds_length": 3093,
"cdna_start": 2465,
"cdna_end": null,
"cdna_length": 3428,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"hgvs_c": "c.2215C>T",
"hgvs_p": "p.Leu739Leu",
"transcript": "ENST00000674046.1",
"protein_id": "ENSP00000501174.1",
"transcript_support_level": null,
"aa_start": 739,
"aa_end": null,
"aa_length": 1001,
"cds_start": 2215,
"cds_end": null,
"cds_length": 3006,
"cdna_start": 2465,
"cdna_end": null,
"cdna_length": 14695,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"hgvs_c": "c.2215C>T",
"hgvs_p": "p.Leu739Leu",
"transcript": "ENST00000635828.1",
"protein_id": "ENSP00000490170.1",
"transcript_support_level": 5,
"aa_start": 739,
"aa_end": null,
"aa_length": 881,
"cds_start": 2215,
"cds_end": null,
"cds_length": 2646,
"cdna_start": 2581,
"cdna_end": null,
"cdna_length": 3823,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"hgvs_c": "c.2215C>T",
"hgvs_p": "p.Leu739Leu",
"transcript": "ENST00000463994.4",
"protein_id": "ENSP00000485184.1",
"transcript_support_level": 5,
"aa_start": 739,
"aa_end": null,
"aa_length": 783,
"cds_start": 2215,
"cds_end": null,
"cds_length": 2354,
"cdna_start": 2493,
"cdna_end": null,
"cdna_length": 2632,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"dbsnp": "rs747554139",
"frequency_reference_population": 0.0000075272424,
"hom_count_reference_population": 7,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000737333,
"gnomad_genomes_af": 0.0000090362,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.46000000834465027,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.10999999940395355,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.065,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.11,
"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": -11,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -11,
"benign_score": 11,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000623535.2",
"gene_symbol": "CDKL5",
"hgnc_id": 11411,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL,AD",
"hgvs_c": "c.2215C>T",
"hgvs_p": "p.Leu739Leu"
}
],
"clinvar_disease": " 2,Angelman syndrome-like,Developmental and epileptic encephalopathy,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 B:1",
"phenotype_combined": "not specified|Developmental and epileptic encephalopathy, 2;Angelman syndrome-like",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}