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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: 1-23804480-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=23804480&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 23804480,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000374490.8",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCL",
"gene_hgnc_id": 5005,
"hgvs_c": "c.796T>C",
"hgvs_p": "p.Cys266Arg",
"transcript": "NM_000191.3",
"protein_id": "NP_000182.2",
"transcript_support_level": null,
"aa_start": 266,
"aa_end": null,
"aa_length": 325,
"cds_start": 796,
"cds_end": null,
"cds_length": 978,
"cdna_start": 810,
"cdna_end": null,
"cdna_length": 1570,
"mane_select": "ENST00000374490.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCL",
"gene_hgnc_id": 5005,
"hgvs_c": "c.796T>C",
"hgvs_p": "p.Cys266Arg",
"transcript": "ENST00000374490.8",
"protein_id": "ENSP00000363614.3",
"transcript_support_level": 1,
"aa_start": 266,
"aa_end": null,
"aa_length": 325,
"cds_start": 796,
"cds_end": null,
"cds_length": 978,
"cdna_start": 810,
"cdna_end": null,
"cdna_length": 1570,
"mane_select": "NM_000191.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCL",
"gene_hgnc_id": 5005,
"hgvs_c": "n.487T>C",
"hgvs_p": null,
"transcript": "ENST00000509389.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 1379,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCL",
"gene_hgnc_id": 5005,
"hgvs_c": "c.583T>C",
"hgvs_p": "p.Cys195Arg",
"transcript": "NM_001166059.2",
"protein_id": "NP_001159531.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 254,
"cds_start": 583,
"cds_end": null,
"cds_length": 765,
"cdna_start": 597,
"cdna_end": null,
"cdna_length": 1357,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCL",
"gene_hgnc_id": 5005,
"hgvs_c": "c.583T>C",
"hgvs_p": "p.Cys195Arg",
"transcript": "ENST00000436439.6",
"protein_id": "ENSP00000389281.2",
"transcript_support_level": 2,
"aa_start": 195,
"aa_end": null,
"aa_length": 254,
"cds_start": 583,
"cds_end": null,
"cds_length": 765,
"cdna_start": 596,
"cdna_end": null,
"cdna_length": 1354,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCL",
"gene_hgnc_id": 5005,
"hgvs_c": "c.364T>C",
"hgvs_p": "p.Cys122Arg",
"transcript": "ENST00000235958.4",
"protein_id": "ENSP00000235958.4",
"transcript_support_level": 5,
"aa_start": 122,
"aa_end": null,
"aa_length": 181,
"cds_start": 364,
"cds_end": null,
"cds_length": 546,
"cdna_start": 366,
"cdna_end": null,
"cdna_length": 1101,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCL",
"gene_hgnc_id": 5005,
"hgvs_c": "n.1393T>C",
"hgvs_p": null,
"transcript": "ENST00000374487.6",
"protein_id": null,
"transcript_support_level": 2,
"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": 2151,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HMGCL",
"gene_hgnc_id": 5005,
"dbsnp": "rs757884073",
"frequency_reference_population": 0.000003097928,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000273639,
"gnomad_genomes_af": 0.00000657013,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.995412290096283,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.986,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9803,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.61,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.232,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.02,
"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": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP2,PP3_Strong,PP5_Moderate",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PM2",
"PP2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000374490.8",
"gene_symbol": "HMGCL",
"hgnc_id": 5005,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.796T>C",
"hgvs_p": "p.Cys266Arg"
}
],
"clinvar_disease": "Deficiency of hydroxymethylglutaryl-CoA lyase",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Deficiency of hydroxymethylglutaryl-CoA lyase",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}