← Back to variant description
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: 6-28532328-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=28532328&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 28532328,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001509.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPX5",
"gene_hgnc_id": 4557,
"hgvs_c": "c.367C>T",
"hgvs_p": "p.Arg123Cys",
"transcript": "NM_001509.3",
"protein_id": "NP_001500.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 221,
"cds_start": 367,
"cds_end": null,
"cds_length": 666,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000412168.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001509.3"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPX5",
"gene_hgnc_id": 4557,
"hgvs_c": "c.367C>T",
"hgvs_p": "p.Arg123Cys",
"transcript": "ENST00000412168.7",
"protein_id": "ENSP00000392398.2",
"transcript_support_level": 1,
"aa_start": 123,
"aa_end": null,
"aa_length": 221,
"cds_start": 367,
"cds_end": null,
"cds_length": 666,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001509.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000412168.7"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPX5",
"gene_hgnc_id": 4557,
"hgvs_c": "c.249C>T",
"hgvs_p": "p.Ser83Ser",
"transcript": "ENST00000469384.1",
"protein_id": "ENSP00000419935.1",
"transcript_support_level": 1,
"aa_start": 83,
"aa_end": null,
"aa_length": 100,
"cds_start": 249,
"cds_end": null,
"cds_length": 303,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000469384.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPX5",
"gene_hgnc_id": 4557,
"hgvs_c": "c.249C>T",
"hgvs_p": "p.Ser83Ser",
"transcript": "NM_003996.3",
"protein_id": "NP_003987.2",
"transcript_support_level": null,
"aa_start": 83,
"aa_end": null,
"aa_length": 100,
"cds_start": 249,
"cds_end": null,
"cds_length": 303,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003996.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPX5",
"gene_hgnc_id": 4557,
"hgvs_c": "n.742C>T",
"hgvs_p": null,
"transcript": "ENST00000442674.6",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000442674.6"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPX5",
"gene_hgnc_id": 4557,
"hgvs_c": "n.440C>T",
"hgvs_p": null,
"transcript": "ENST00000483784.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000483784.1"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPX5",
"gene_hgnc_id": 4557,
"hgvs_c": "n.445C>T",
"hgvs_p": null,
"transcript": "NR_144470.2",
"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": "NR_144470.2"
}
],
"gene_symbol": "GPX5",
"gene_hgnc_id": 4557,
"dbsnp": "rs1213371172",
"frequency_reference_population": 0.000022342347,
"hom_count_reference_population": 0,
"allele_count_reference_population": 35,
"gnomad_exomes_af": 0.000020504,
"gnomad_genomes_af": 0.000039428,
"gnomad_exomes_ac": 29,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7745914459228516,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.18000000715255737,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.257,
"revel_prediction": "Benign",
"alphamissense_score": 0.6542,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.18,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.411,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.18,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 0,
"pathogenic_score": 1,
"criteria": [
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001509.3",
"gene_symbol": "GPX5",
"hgnc_id": 4557,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.367C>T",
"hgvs_p": "p.Arg123Cys"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}