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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: 1-203682799-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=203682799&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 203682799,
"ref": "T",
"alt": "C",
"effect": "5_prime_UTR_variant",
"transcript": "ENST00000357681.10",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2B4",
"gene_hgnc_id": 817,
"hgvs_c": "c.-407T>C",
"hgvs_p": null,
"transcript": "NM_001684.5",
"protein_id": "NP_001675.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1205,
"cds_start": -4,
"cds_end": null,
"cds_length": 3618,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8697,
"mane_select": "ENST00000357681.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2B4",
"gene_hgnc_id": 817,
"hgvs_c": "c.-407T>C",
"hgvs_p": null,
"transcript": "ENST00000357681.10",
"protein_id": "ENSP00000350310.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1205,
"cds_start": -4,
"cds_end": null,
"cds_length": 3618,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8697,
"mane_select": "NM_001684.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2B4",
"gene_hgnc_id": 817,
"hgvs_c": "c.-407T>C",
"hgvs_p": null,
"transcript": "ENST00000341360.7",
"protein_id": "ENSP00000340930.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1170,
"cds_start": -4,
"cds_end": null,
"cds_length": 3513,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8875,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2B4",
"gene_hgnc_id": 817,
"hgvs_c": "c.-407T>C",
"hgvs_p": null,
"transcript": "NM_001001396.3",
"protein_id": "NP_001001396.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1170,
"cds_start": -4,
"cds_end": null,
"cds_length": 3513,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8875,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2B4",
"gene_hgnc_id": 817,
"hgvs_c": "c.-407T>C",
"hgvs_p": null,
"transcript": "NM_001365783.2",
"protein_id": "NP_001352712.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1164,
"cds_start": -4,
"cds_end": null,
"cds_length": 3495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4568,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2B4",
"gene_hgnc_id": 817,
"hgvs_c": "c.-407T>C",
"hgvs_p": null,
"transcript": "NM_001365784.2",
"protein_id": "NP_001352713.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1164,
"cds_start": -4,
"cds_end": null,
"cds_length": 3495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4325,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2B4",
"gene_hgnc_id": 817,
"hgvs_c": "c.-407T>C",
"hgvs_p": null,
"transcript": "ENST00000705901.1",
"protein_id": "ENSP00000516177.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1158,
"cds_start": -4,
"cds_end": null,
"cds_length": 3477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5498,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATP2B4",
"gene_hgnc_id": 817,
"dbsnp": "rs1541252",
"frequency_reference_population": 0.83292145,
"hom_count_reference_population": 55040,
"allele_count_reference_population": 130094,
"gnomad_exomes_af": 0.84742,
"gnomad_genomes_af": 0.832534,
"gnomad_exomes_ac": 3449,
"gnomad_genomes_ac": 126645,
"gnomad_exomes_homalt": 1491,
"gnomad_genomes_homalt": 53549,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8100000023841858,
"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": -0.81,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.072,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000357681.10",
"gene_symbol": "ATP2B4",
"hgnc_id": 817,
"effects": [
"5_prime_UTR_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.-407T>C",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}