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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: 3-32140306-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=32140306&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 32140306,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000282541.10",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPD1L",
"gene_hgnc_id": 28956,
"hgvs_c": "c.445C>T",
"hgvs_p": "p.Leu149Leu",
"transcript": "NM_015141.4",
"protein_id": "NP_055956.1",
"transcript_support_level": null,
"aa_start": 149,
"aa_end": null,
"aa_length": 351,
"cds_start": 445,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 537,
"cdna_end": null,
"cdna_length": 3947,
"mane_select": "ENST00000282541.10",
"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": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPD1L",
"gene_hgnc_id": 28956,
"hgvs_c": "c.445C>T",
"hgvs_p": "p.Leu149Leu",
"transcript": "ENST00000282541.10",
"protein_id": "ENSP00000282541.6",
"transcript_support_level": 1,
"aa_start": 149,
"aa_end": null,
"aa_length": 351,
"cds_start": 445,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 537,
"cdna_end": null,
"cdna_length": 3947,
"mane_select": "NM_015141.4",
"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": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPD1L",
"gene_hgnc_id": 28956,
"hgvs_c": "c.304C>T",
"hgvs_p": "p.Leu102Leu",
"transcript": "ENST00000425459.5",
"protein_id": "ENSP00000408770.1",
"transcript_support_level": 4,
"aa_start": 102,
"aa_end": null,
"aa_length": 172,
"cds_start": 304,
"cds_end": null,
"cds_length": 520,
"cdna_start": 383,
"cdna_end": null,
"cdna_length": 599,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPD1L",
"gene_hgnc_id": 28956,
"hgvs_c": "c.328C>T",
"hgvs_p": "p.Leu110Leu",
"transcript": "ENST00000431009.1",
"protein_id": "ENSP00000416518.1",
"transcript_support_level": 4,
"aa_start": 110,
"aa_end": null,
"aa_length": 143,
"cds_start": 328,
"cds_end": null,
"cds_length": 432,
"cdna_start": 517,
"cdna_end": null,
"cdna_length": 621,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPD1L",
"gene_hgnc_id": 28956,
"hgvs_c": "c.328C>T",
"hgvs_p": "p.Leu110Leu",
"transcript": "ENST00000429432.5",
"protein_id": "ENSP00000393861.1",
"transcript_support_level": 4,
"aa_start": 110,
"aa_end": null,
"aa_length": 126,
"cds_start": 328,
"cds_end": null,
"cds_length": 383,
"cdna_start": 539,
"cdna_end": null,
"cdna_length": 594,
"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": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPD1L",
"gene_hgnc_id": 28956,
"hgvs_c": "c.304C>T",
"hgvs_p": "p.Leu102Leu",
"transcript": "XM_006713068.3",
"protein_id": "XP_006713131.1",
"transcript_support_level": null,
"aa_start": 102,
"aa_end": null,
"aa_length": 304,
"cds_start": 304,
"cds_end": null,
"cds_length": 915,
"cdna_start": 396,
"cdna_end": null,
"cdna_length": 3806,
"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": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPD1L",
"gene_hgnc_id": 28956,
"hgvs_c": "n.*72C>T",
"hgvs_p": null,
"transcript": "ENST00000428684.1",
"protein_id": "ENSP00000392199.1",
"transcript_support_level": 5,
"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": 822,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPD1L",
"gene_hgnc_id": 28956,
"hgvs_c": "n.*72C>T",
"hgvs_p": null,
"transcript": "ENST00000428684.1",
"protein_id": "ENSP00000392199.1",
"transcript_support_level": 5,
"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": 822,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GPD1L",
"gene_hgnc_id": 28956,
"dbsnp": "rs146738300",
"frequency_reference_population": 0.00027569066,
"hom_count_reference_population": 0,
"allele_count_reference_population": 445,
"gnomad_exomes_af": 0.000288679,
"gnomad_genomes_af": 0.000151022,
"gnomad_exomes_ac": 422,
"gnomad_genomes_ac": 23,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.3799999952316284,
"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": -0.38,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.361,
"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": -15,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BS2",
"acmg_by_gene": [
{
"score": -15,
"benign_score": 15,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000282541.10",
"gene_symbol": "GPD1L",
"hgnc_id": 28956,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.445C>T",
"hgvs_p": "p.Leu149Leu"
}
],
"clinvar_disease": "Brugada syndrome,Cardiovascular phenotype,not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4",
"phenotype_combined": "Brugada syndrome|not provided|Cardiovascular phenotype",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}