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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: 16-71649426-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=71649426&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 71649426,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_015020.3",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHLPP2",
"gene_hgnc_id": 29149,
"hgvs_c": "c.3436G>A",
"hgvs_p": "p.Gly1146Ser",
"transcript": "NM_015020.3",
"protein_id": "NP_055835.2",
"transcript_support_level": null,
"aa_start": 1146,
"aa_end": null,
"aa_length": 1323,
"cds_start": 3436,
"cds_end": null,
"cds_length": 3972,
"cdna_start": 3815,
"cdna_end": null,
"cdna_length": 8317,
"mane_select": "ENST00000568954.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHLPP2",
"gene_hgnc_id": 29149,
"hgvs_c": "c.3436G>A",
"hgvs_p": "p.Gly1146Ser",
"transcript": "ENST00000568954.5",
"protein_id": "ENSP00000457991.1",
"transcript_support_level": 1,
"aa_start": 1146,
"aa_end": null,
"aa_length": 1323,
"cds_start": 3436,
"cds_end": null,
"cds_length": 3972,
"cdna_start": 3815,
"cdna_end": null,
"cdna_length": 8317,
"mane_select": "NM_015020.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "PHLPP2",
"gene_hgnc_id": 29149,
"hgvs_c": "n.2031+3364G>A",
"hgvs_p": null,
"transcript": "ENST00000568004.5",
"protein_id": "ENSP00000458660.1",
"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": 3099,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHLPP2",
"gene_hgnc_id": 29149,
"hgvs_c": "c.3541G>A",
"hgvs_p": "p.Gly1181Ser",
"transcript": "ENST00000567016.1",
"protein_id": "ENSP00000454519.1",
"transcript_support_level": 5,
"aa_start": 1181,
"aa_end": null,
"aa_length": 1358,
"cds_start": 3541,
"cds_end": null,
"cds_length": 4077,
"cdna_start": 3556,
"cdna_end": null,
"cdna_length": 4812,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHLPP2",
"gene_hgnc_id": 29149,
"hgvs_c": "c.3235G>A",
"hgvs_p": "p.Gly1079Ser",
"transcript": "NM_001289003.1",
"protein_id": "NP_001275932.1",
"transcript_support_level": null,
"aa_start": 1079,
"aa_end": null,
"aa_length": 1256,
"cds_start": 3235,
"cds_end": null,
"cds_length": 3771,
"cdna_start": 3961,
"cdna_end": null,
"cdna_length": 8463,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHLPP2",
"gene_hgnc_id": 29149,
"hgvs_c": "c.3235G>A",
"hgvs_p": "p.Gly1079Ser",
"transcript": "ENST00000393524.6",
"protein_id": "ENSP00000377159.2",
"transcript_support_level": 2,
"aa_start": 1079,
"aa_end": null,
"aa_length": 1256,
"cds_start": 3235,
"cds_end": null,
"cds_length": 3771,
"cdna_start": 3969,
"cdna_end": null,
"cdna_length": 8467,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PHLPP2",
"gene_hgnc_id": 29149,
"hgvs_c": "n.903+3364G>A",
"hgvs_p": null,
"transcript": "ENST00000564884.5",
"protein_id": "ENSP00000456572.1",
"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": 2077,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PHLPP2",
"gene_hgnc_id": 29149,
"dbsnp": "rs551193903",
"frequency_reference_population": 0.000014250716,
"hom_count_reference_population": 0,
"allele_count_reference_population": 23,
"gnomad_exomes_af": 0.0000136815,
"gnomad_genomes_af": 0.00001972,
"gnomad_exomes_ac": 20,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5695192217826843,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.368,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5001,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.1,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.713,
"phylop100way_prediction": "Pathogenic",
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_015020.3",
"gene_symbol": "PHLPP2",
"hgnc_id": 29149,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3436G>A",
"hgvs_p": "p.Gly1146Ser"
}
],
"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
}