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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: 2-31529459-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=31529459&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 31529459,
"ref": "T",
"alt": "G",
"effect": "splice_acceptor_variant,intron_variant",
"transcript": "NM_000348.4",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SRD5A2",
"gene_hgnc_id": 11285,
"hgvs_c": "c.548-2A>C",
"hgvs_p": null,
"transcript": "NM_000348.4",
"protein_id": "NP_000339.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 254,
"cds_start": null,
"cds_end": null,
"cds_length": 765,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000622030.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000348.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SRD5A2",
"gene_hgnc_id": 11285,
"hgvs_c": "c.548-2A>C",
"hgvs_p": null,
"transcript": "ENST00000622030.2",
"protein_id": "ENSP00000477587.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 254,
"cds_start": null,
"cds_end": null,
"cds_length": 765,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000348.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000622030.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "SRD5A2",
"gene_hgnc_id": 11285,
"hgvs_c": "c.650-2A>C",
"hgvs_p": null,
"transcript": "ENST00000882642.1",
"protein_id": "ENSP00000552701.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 288,
"cds_start": null,
"cds_end": null,
"cds_length": 867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882642.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SRD5A2",
"gene_hgnc_id": 11285,
"hgvs_c": "c.446-2A>C",
"hgvs_p": null,
"transcript": "ENST00000882643.1",
"protein_id": "ENSP00000552702.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 220,
"cds_start": null,
"cds_end": null,
"cds_length": 663,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882643.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SRD5A2",
"gene_hgnc_id": 11285,
"hgvs_c": "c.326-2A>C",
"hgvs_p": null,
"transcript": "XM_011533069.3",
"protein_id": "XP_011531371.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 180,
"cds_start": null,
"cds_end": null,
"cds_length": 543,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533069.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SRD5A2",
"gene_hgnc_id": 11285,
"hgvs_c": "c.293-2A>C",
"hgvs_p": null,
"transcript": "XM_011533072.3",
"protein_id": "XP_011531374.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 169,
"cds_start": null,
"cds_end": null,
"cds_length": 510,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533072.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000228563",
"gene_hgnc_id": null,
"hgvs_c": "n.255+1759T>G",
"hgvs_p": null,
"transcript": "ENST00000435713.1",
"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": "ENST00000435713.1"
}
],
"gene_symbol": "SRD5A2",
"gene_hgnc_id": 11285,
"dbsnp": "rs61750397",
"frequency_reference_population": 0.000047755373,
"hom_count_reference_population": 0,
"allele_count_reference_population": 77,
"gnomad_exomes_af": 0.0000499933,
"gnomad_genomes_af": 0.0000262833,
"gnomad_exomes_ac": 73,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.23999999463558197,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.6600000262260437,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.24,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.957,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.66,
"spliceai_max_prediction": "Pathogenic",
"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_000348.4",
"gene_symbol": "SRD5A2",
"hgnc_id": 11285,
"effects": [
"splice_acceptor_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.548-2A>C",
"hgvs_p": null
},
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM2",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000435713.1",
"gene_symbol": "ENSG00000228563",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.255+1759T>G",
"hgvs_p": null
}
],
"clinvar_disease": "3-Oxo-5 alpha-steroid delta 4-dehydrogenase deficiency,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:2 O:1",
"phenotype_combined": "not provided|3-Oxo-5 alpha-steroid delta 4-dehydrogenase deficiency",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}