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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: 1-119415434-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=119415434&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 119415434,
"ref": "C",
"alt": "A",
"effect": "stop_gained",
"transcript": "NM_000198.4",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD3B2",
"gene_hgnc_id": 5218,
"hgvs_c": "c.15C>A",
"hgvs_p": "p.Cys5*",
"transcript": "NM_000198.4",
"protein_id": "NP_000189.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 372,
"cds_start": 15,
"cds_end": null,
"cds_length": 1119,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000369416.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000198.4"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD3B2",
"gene_hgnc_id": 5218,
"hgvs_c": "c.15C>A",
"hgvs_p": "p.Cys5*",
"transcript": "ENST00000369416.4",
"protein_id": "ENSP00000358424.3",
"transcript_support_level": 1,
"aa_start": 5,
"aa_end": null,
"aa_length": 372,
"cds_start": 15,
"cds_end": null,
"cds_length": 1119,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000198.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000369416.4"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD3B2",
"gene_hgnc_id": 5218,
"hgvs_c": "c.15C>A",
"hgvs_p": "p.Cys5*",
"transcript": "NM_001166120.2",
"protein_id": "NP_001159592.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 372,
"cds_start": 15,
"cds_end": null,
"cds_length": 1119,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001166120.2"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD3B2",
"gene_hgnc_id": 5218,
"hgvs_c": "c.15C>A",
"hgvs_p": "p.Cys5*",
"transcript": "ENST00000543831.5",
"protein_id": "ENSP00000445122.1",
"transcript_support_level": 3,
"aa_start": 5,
"aa_end": null,
"aa_length": 372,
"cds_start": 15,
"cds_end": null,
"cds_length": 1119,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000543831.5"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD3B2",
"gene_hgnc_id": 5218,
"hgvs_c": "c.15C>A",
"hgvs_p": "p.Cys5*",
"transcript": "ENST00000902254.1",
"protein_id": "ENSP00000572313.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 372,
"cds_start": 15,
"cds_end": null,
"cds_length": 1119,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902254.1"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD3B2",
"gene_hgnc_id": 5218,
"hgvs_c": "c.15C>A",
"hgvs_p": "p.Cys5*",
"transcript": "ENST00000948746.1",
"protein_id": "ENSP00000618805.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 372,
"cds_start": 15,
"cds_end": null,
"cds_length": 1119,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948746.1"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD3B2",
"gene_hgnc_id": 5218,
"hgvs_c": "c.15C>A",
"hgvs_p": "p.Cys5*",
"transcript": "ENST00000948747.1",
"protein_id": "ENSP00000618806.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 372,
"cds_start": 15,
"cds_end": null,
"cds_length": 1119,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948747.1"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD3B2",
"gene_hgnc_id": 5218,
"hgvs_c": "c.15C>A",
"hgvs_p": "p.Cys5*",
"transcript": "ENST00000948748.1",
"protein_id": "ENSP00000618807.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 372,
"cds_start": 15,
"cds_end": null,
"cds_length": 1119,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948748.1"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD3B2",
"gene_hgnc_id": 5218,
"hgvs_c": "c.15C>A",
"hgvs_p": "p.Cys5*",
"transcript": "ENST00000948749.1",
"protein_id": "ENSP00000618808.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 317,
"cds_start": 15,
"cds_end": null,
"cds_length": 954,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948749.1"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD3B2",
"gene_hgnc_id": 5218,
"hgvs_c": "c.15C>A",
"hgvs_p": "p.Cys5*",
"transcript": "ENST00000433745.5",
"protein_id": "ENSP00000388292.1",
"transcript_support_level": 3,
"aa_start": 5,
"aa_end": null,
"aa_length": 194,
"cds_start": 15,
"cds_end": null,
"cds_length": 587,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000433745.5"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD3B2",
"gene_hgnc_id": 5218,
"hgvs_c": "n.144C>A",
"hgvs_p": null,
"transcript": "ENST00000443865.2",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000443865.2"
},
{
"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": "HSD3B2",
"gene_hgnc_id": 5218,
"hgvs_c": "n.156C>A",
"hgvs_p": null,
"transcript": "ENST00000471656.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000471656.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "ENSG00000307032",
"gene_hgnc_id": null,
"hgvs_c": "n.387G>T",
"hgvs_p": null,
"transcript": "ENST00000823009.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000823009.1"
}
],
"gene_symbol": "HSD3B2",
"gene_hgnc_id": 5218,
"dbsnp": "rs766474996",
"frequency_reference_population": 0.000040897008,
"hom_count_reference_population": 0,
"allele_count_reference_population": 66,
"gnomad_exomes_af": 0.0000431013,
"gnomad_genomes_af": 0.0000197189,
"gnomad_exomes_ac": 63,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5400000214576721,
"computational_prediction_selected": "Pathogenic",
"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": 0.54,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.102,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_000198.4",
"gene_symbol": "HSD3B2",
"hgnc_id": 5218,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.15C>A",
"hgvs_p": "p.Cys5*"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000823009.1",
"gene_symbol": "ENSG00000307032",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.387G>T",
"hgvs_p": null
}
],
"clinvar_disease": "3 beta-Hydroxysteroid dehydrogenase deficiency,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"phenotype_combined": "3 beta-Hydroxysteroid dehydrogenase deficiency|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}