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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-18650553-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=18650553&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 18650553,
"ref": "C",
"alt": "G",
"effect": "intron_variant",
"transcript": "ENST00000379984.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"hgvs_c": "c.2941C>G",
"hgvs_p": "p.Arg981Gly",
"transcript": "ENST00000379989.6",
"protein_id": "ENSP00000369325.3",
"transcript_support_level": 1,
"aa_start": 981,
"aa_end": null,
"aa_length": 1030,
"cds_start": 2941,
"cds_end": null,
"cds_length": 3093,
"cdna_start": 3226,
"cdna_end": null,
"cdna_length": 3463,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"hgvs_c": "c.2941C>G",
"hgvs_p": "p.Arg981Gly",
"transcript": "ENST00000379996.7",
"protein_id": "ENSP00000369332.3",
"transcript_support_level": 1,
"aa_start": 981,
"aa_end": null,
"aa_length": 1030,
"cds_start": 2941,
"cds_end": null,
"cds_length": 3093,
"cdna_start": 3216,
"cdna_end": null,
"cdna_length": 3449,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RS1",
"gene_hgnc_id": 10457,
"hgvs_c": "c.185-3221G>C",
"hgvs_p": null,
"transcript": "NM_000330.4",
"protein_id": "NP_000321.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 224,
"cds_start": -4,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3031,
"mane_select": "ENST00000379984.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RS1",
"gene_hgnc_id": 10457,
"hgvs_c": "c.185-3221G>C",
"hgvs_p": null,
"transcript": "ENST00000379984.4",
"protein_id": "ENSP00000369320.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 224,
"cds_start": -4,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3031,
"mane_select": "NM_000330.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"hgvs_c": "c.2941C>G",
"hgvs_p": "p.Arg981Gly",
"transcript": "NM_001037343.2",
"protein_id": "NP_001032420.1",
"transcript_support_level": null,
"aa_start": 981,
"aa_end": null,
"aa_length": 1030,
"cds_start": 2941,
"cds_end": null,
"cds_length": 3093,
"cdna_start": 3190,
"cdna_end": null,
"cdna_length": 3427,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"hgvs_c": "c.2941C>G",
"hgvs_p": "p.Arg981Gly",
"transcript": "NM_003159.3",
"protein_id": "NP_003150.1",
"transcript_support_level": null,
"aa_start": 981,
"aa_end": null,
"aa_length": 1030,
"cds_start": 2941,
"cds_end": null,
"cds_length": 3093,
"cdna_start": 3191,
"cdna_end": null,
"cdna_length": 3428,
"mane_select": null,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"hgvs_c": "n.213C>G",
"hgvs_p": null,
"transcript": "ENST00000673617.1",
"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": 378,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RS1",
"gene_hgnc_id": 10457,
"hgvs_c": "c.-170G>C",
"hgvs_p": null,
"transcript": "XM_047442337.1",
"protein_id": "XP_047298293.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 192,
"cds_start": -4,
"cds_end": null,
"cds_length": 579,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2922,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RS1",
"gene_hgnc_id": 10457,
"hgvs_c": "n.-16G>C",
"hgvs_p": null,
"transcript": "ENST00000476595.1",
"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": 1246,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RS1",
"gene_hgnc_id": 10457,
"dbsnp": "rs374054249",
"frequency_reference_population": 0.00006441809,
"hom_count_reference_population": 28,
"allele_count_reference_population": 78,
"gnomad_exomes_af": 0.0000673858,
"gnomad_genomes_af": 0.0000354972,
"gnomad_exomes_ac": 74,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.13978299498558044,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.078,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.077,
"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": -14,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000379984.4",
"gene_symbol": "RS1",
"hgnc_id": 10457,
"effects": [
"intron_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.185-3221G>C",
"hgvs_p": null
},
{
"score": -18,
"benign_score": 18,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_003159.3",
"gene_symbol": "CDKL5",
"hgnc_id": 11411,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL,AD",
"hgvs_c": "c.2941C>G",
"hgvs_p": "p.Arg981Gly"
}
],
"clinvar_disease": " 2,Angelman syndrome-like,CDKL5 disorder,Developmental and epileptic encephalopathy,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "US:1 LB:3 B:1",
"phenotype_combined": "Angelman syndrome-like;Developmental and epileptic encephalopathy, 2|not provided|Developmental and epileptic encephalopathy, 2|CDKL5 disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}