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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-18642103-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=18642103&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 18642103,
"ref": "G",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000379984.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RS1",
"gene_hgnc_id": 10457,
"hgvs_c": "c.576C>A",
"hgvs_p": "p.Pro192Pro",
"transcript": "NM_000330.4",
"protein_id": "NP_000321.1",
"transcript_support_level": null,
"aa_start": 192,
"aa_end": null,
"aa_length": 224,
"cds_start": 576,
"cds_end": null,
"cds_length": 675,
"cdna_start": 616,
"cdna_end": null,
"cdna_length": 3031,
"mane_select": "ENST00000379984.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RS1",
"gene_hgnc_id": 10457,
"hgvs_c": "c.576C>A",
"hgvs_p": "p.Pro192Pro",
"transcript": "ENST00000379984.4",
"protein_id": "ENSP00000369320.3",
"transcript_support_level": 1,
"aa_start": 192,
"aa_end": null,
"aa_length": 224,
"cds_start": 576,
"cds_end": null,
"cds_length": 675,
"cdna_start": 616,
"cdna_end": null,
"cdna_length": 3031,
"mane_select": "NM_000330.4",
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RS1",
"gene_hgnc_id": 10457,
"hgvs_c": "n.1067C>A",
"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
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"hgvs_c": "c.2714-3904G>T",
"hgvs_p": null,
"transcript": "ENST00000379989.6",
"protein_id": "ENSP00000369325.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1030,
"cds_start": -4,
"cds_end": null,
"cds_length": 3093,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3463,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"hgvs_c": "c.2714-3904G>T",
"hgvs_p": null,
"transcript": "ENST00000379996.7",
"protein_id": "ENSP00000369332.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1030,
"cds_start": -4,
"cds_end": null,
"cds_length": 3093,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3449,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RS1",
"gene_hgnc_id": 10457,
"hgvs_c": "c.480C>A",
"hgvs_p": "p.Pro160Pro",
"transcript": "XM_047442337.1",
"protein_id": "XP_047298293.1",
"transcript_support_level": null,
"aa_start": 160,
"aa_end": null,
"aa_length": 192,
"cds_start": 480,
"cds_end": null,
"cds_length": 579,
"cdna_start": 736,
"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": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"hgvs_c": "c.2714-3904G>T",
"hgvs_p": null,
"transcript": "NM_001037343.2",
"protein_id": "NP_001032420.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1030,
"cds_start": -4,
"cds_end": null,
"cds_length": 3093,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3427,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"hgvs_c": "c.2714-3904G>T",
"hgvs_p": null,
"transcript": "NM_003159.3",
"protein_id": "NP_003150.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1030,
"cds_start": -4,
"cds_end": null,
"cds_length": 3093,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3428,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RS1",
"gene_hgnc_id": 10457,
"dbsnp": "rs186334493",
"frequency_reference_population": 9.1074264e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 9.10743e-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": -0.5799999833106995,
"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": -0.58,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.416,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 7,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000379984.4",
"gene_symbol": "RS1",
"hgnc_id": 10457,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.576C>A",
"hgvs_p": "p.Pro192Pro"
},
{
"score": -4,
"benign_score": 6,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_003159.3",
"gene_symbol": "CDKL5",
"hgnc_id": 11411,
"effects": [
"intron_variant"
],
"inheritance_mode": "XL,AD",
"hgvs_c": "c.2714-3904G>T",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}