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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-100402721-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=100402721&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 100402721,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000373034.8",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH19",
"gene_hgnc_id": 14270,
"hgvs_c": "c.2419C>A",
"hgvs_p": "p.Leu807Met",
"transcript": "NM_001184880.2",
"protein_id": "NP_001171809.1",
"transcript_support_level": null,
"aa_start": 807,
"aa_end": null,
"aa_length": 1148,
"cds_start": 2419,
"cds_end": null,
"cds_length": 3447,
"cdna_start": 4095,
"cdna_end": null,
"cdna_length": 9756,
"mane_select": "ENST00000373034.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH19",
"gene_hgnc_id": 14270,
"hgvs_c": "c.2419C>A",
"hgvs_p": "p.Leu807Met",
"transcript": "ENST00000373034.8",
"protein_id": "ENSP00000362125.4",
"transcript_support_level": 1,
"aa_start": 807,
"aa_end": null,
"aa_length": 1148,
"cds_start": 2419,
"cds_end": null,
"cds_length": 3447,
"cdna_start": 4095,
"cdna_end": null,
"cdna_length": 9756,
"mane_select": "NM_001184880.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH19",
"gene_hgnc_id": 14270,
"hgvs_c": "c.2278C>A",
"hgvs_p": "p.Leu760Met",
"transcript": "ENST00000255531.8",
"protein_id": "ENSP00000255531.7",
"transcript_support_level": 1,
"aa_start": 760,
"aa_end": null,
"aa_length": 1101,
"cds_start": 2278,
"cds_end": null,
"cds_length": 3306,
"cdna_start": 2278,
"cdna_end": null,
"cdna_length": 7937,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH19",
"gene_hgnc_id": 14270,
"hgvs_c": "c.2278C>A",
"hgvs_p": "p.Leu760Met",
"transcript": "ENST00000420881.6",
"protein_id": "ENSP00000400327.2",
"transcript_support_level": 1,
"aa_start": 760,
"aa_end": null,
"aa_length": 1100,
"cds_start": 2278,
"cds_end": null,
"cds_length": 3303,
"cdna_start": 2278,
"cdna_end": null,
"cdna_length": 7936,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH19",
"gene_hgnc_id": 14270,
"hgvs_c": "c.2278C>A",
"hgvs_p": "p.Leu760Met",
"transcript": "NM_001105243.2",
"protein_id": "NP_001098713.1",
"transcript_support_level": null,
"aa_start": 760,
"aa_end": null,
"aa_length": 1101,
"cds_start": 2278,
"cds_end": null,
"cds_length": 3306,
"cdna_start": 3954,
"cdna_end": null,
"cdna_length": 9615,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCDH19",
"gene_hgnc_id": 14270,
"hgvs_c": "c.2278C>A",
"hgvs_p": "p.Leu760Met",
"transcript": "NM_020766.3",
"protein_id": "NP_065817.2",
"transcript_support_level": null,
"aa_start": 760,
"aa_end": null,
"aa_length": 1100,
"cds_start": 2278,
"cds_end": null,
"cds_length": 3303,
"cdna_start": 3954,
"cdna_end": null,
"cdna_length": 9612,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PCDH19",
"gene_hgnc_id": 14270,
"hgvs_c": "c.66-146C>A",
"hgvs_p": null,
"transcript": "ENST00000636150.1",
"protein_id": "ENSP00000490463.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 52,
"cds_start": -4,
"cds_end": null,
"cds_length": 160,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 160,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PCDH19",
"gene_hgnc_id": 14270,
"dbsnp": "rs1555984464",
"frequency_reference_population": 0.0000016530906,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 9.10976e-7,
"gnomad_genomes_af": 0.00000891814,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3628491163253784,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.202,
"revel_prediction": "Benign",
"alphamissense_score": 0.4886,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.14,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.554,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP2,BP4",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 1,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000373034.8",
"gene_symbol": "PCDH19",
"hgnc_id": 14270,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,XL,Unknown",
"hgvs_c": "c.2419C>A",
"hgvs_p": "p.Leu807Met"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}