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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: 2-31529419-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=31529419&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM1",
"PM5",
"PP2",
"PP3",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SRD5A2",
"hgnc_id": 11285,
"hgvs_c": "c.586G>A",
"hgvs_p": "p.Gly196Ser",
"inheritance_mode": "AR",
"pathogenic_score": 18,
"score": 18,
"transcript": "NM_000348.4",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PS3",
"PP3",
"PP5_Very_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000228563",
"hgnc_id": null,
"hgvs_c": "n.255+1719C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 13,
"score": 13,
"transcript": "ENST00000435713.1",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM1,PM5,PP2,PP3,PP5_Very_Strong",
"acmg_score": 18,
"allele_count_reference_population": 128,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.7153,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.22,
"chr": "2",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": "3-Oxo-5 alpha-steroid delta 4-dehydrogenase deficiency,SRD5A2-related disorder,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:5 LP:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8363708853721619,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 254,
"aa_ref": "G",
"aa_start": 196,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4519,
"cdna_start": 624,
"cds_end": null,
"cds_length": 765,
"cds_start": 586,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_000348.4",
"gene_hgnc_id": 11285,
"gene_symbol": "SRD5A2",
"hgvs_c": "c.586G>A",
"hgvs_p": "p.Gly196Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000622030.2",
"protein_coding": true,
"protein_id": "NP_000339.2",
"strand": false,
"transcript": "NM_000348.4",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 254,
"aa_ref": "G",
"aa_start": 196,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4519,
"cdna_start": 624,
"cds_end": null,
"cds_length": 765,
"cds_start": 586,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000622030.2",
"gene_hgnc_id": 11285,
"gene_symbol": "SRD5A2",
"hgvs_c": "c.586G>A",
"hgvs_p": "p.Gly196Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000348.4",
"protein_coding": true,
"protein_id": "ENSP00000477587.1",
"strand": false,
"transcript": "ENST00000622030.2",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 288,
"aa_ref": "G",
"aa_start": 230,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2579,
"cdna_start": 729,
"cds_end": null,
"cds_length": 867,
"cds_start": 688,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000882642.1",
"gene_hgnc_id": 11285,
"gene_symbol": "SRD5A2",
"hgvs_c": "c.688G>A",
"hgvs_p": "p.Gly230Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000552701.1",
"strand": false,
"transcript": "ENST00000882642.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 220,
"aa_ref": "G",
"aa_start": 162,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2314,
"cdna_start": 525,
"cds_end": null,
"cds_length": 663,
"cds_start": 484,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000882643.1",
"gene_hgnc_id": 11285,
"gene_symbol": "SRD5A2",
"hgvs_c": "c.484G>A",
"hgvs_p": "p.Gly162Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000552702.1",
"strand": false,
"transcript": "ENST00000882643.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 180,
"aa_ref": "G",
"aa_start": 122,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5267,
"cdna_start": 1372,
"cds_end": null,
"cds_length": 543,
"cds_start": 364,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_011533069.3",
"gene_hgnc_id": 11285,
"gene_symbol": "SRD5A2",
"hgvs_c": "c.364G>A",
"hgvs_p": "p.Gly122Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011531371.1",
"strand": false,
"transcript": "XM_011533069.3",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 169,
"aa_ref": "G",
"aa_start": 111,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4654,
"cdna_start": 759,
"cds_end": null,
"cds_length": 510,
"cds_start": 331,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_011533072.3",
"gene_hgnc_id": 11285,
"gene_symbol": "SRD5A2",
"hgvs_c": "c.331G>A",
"hgvs_p": "p.Gly111Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011531374.1",
"strand": false,
"transcript": "XM_011533072.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 646,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000435713.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000228563",
"hgvs_c": "n.255+1719C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000435713.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs121434250",
"effect": "missense_variant",
"frequency_reference_population": 0.0000793158,
"gene_hgnc_id": 11285,
"gene_symbol": "SRD5A2",
"gnomad_exomes_ac": 106,
"gnomad_exomes_af": 0.0000725269,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 22,
"gnomad_genomes_af": 0.000144475,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"phenotype_combined": "3-Oxo-5 alpha-steroid delta 4-dehydrogenase deficiency|not provided|SRD5A2-related disorder",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.845,
"pos": 31529419,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.1899999976158142,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.19,
"transcript": "NM_000348.4"
}
]
}