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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: 1-98953091-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=98953091&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 98953091,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000263177.5",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPPR5",
"gene_hgnc_id": 31703,
"hgvs_c": "c.600C>T",
"hgvs_p": "p.Val200Val",
"transcript": "NM_001037317.2",
"protein_id": "NP_001032394.1",
"transcript_support_level": null,
"aa_start": 200,
"aa_end": null,
"aa_length": 321,
"cds_start": 600,
"cds_end": null,
"cds_length": 966,
"cdna_start": 790,
"cdna_end": null,
"cdna_length": 3983,
"mane_select": "ENST00000263177.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPPR5",
"gene_hgnc_id": 31703,
"hgvs_c": "c.600C>T",
"hgvs_p": "p.Val200Val",
"transcript": "ENST00000263177.5",
"protein_id": "ENSP00000263177.4",
"transcript_support_level": 1,
"aa_start": 200,
"aa_end": null,
"aa_length": 321,
"cds_start": 600,
"cds_end": null,
"cds_length": 966,
"cdna_start": 790,
"cdna_end": null,
"cdna_length": 3983,
"mane_select": "NM_001037317.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPPR5",
"gene_hgnc_id": 31703,
"hgvs_c": "c.600C>T",
"hgvs_p": "p.Val200Val",
"transcript": "ENST00000370188.7",
"protein_id": "ENSP00000359207.3",
"transcript_support_level": 1,
"aa_start": 200,
"aa_end": null,
"aa_length": 316,
"cds_start": 600,
"cds_end": null,
"cds_length": 951,
"cdna_start": 961,
"cdna_end": null,
"cdna_length": 4139,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPPR5",
"gene_hgnc_id": 31703,
"hgvs_c": "c.600C>T",
"hgvs_p": "p.Val200Val",
"transcript": "ENST00000672681.1",
"protein_id": "ENSP00000500930.1",
"transcript_support_level": null,
"aa_start": 200,
"aa_end": null,
"aa_length": 379,
"cds_start": 600,
"cds_end": null,
"cds_length": 1140,
"cdna_start": 961,
"cdna_end": null,
"cdna_length": 4267,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPPR5",
"gene_hgnc_id": 31703,
"hgvs_c": "c.600C>T",
"hgvs_p": "p.Val200Val",
"transcript": "NM_001010861.3",
"protein_id": "NP_001010861.1",
"transcript_support_level": null,
"aa_start": 200,
"aa_end": null,
"aa_length": 316,
"cds_start": 600,
"cds_end": null,
"cds_length": 951,
"cdna_start": 790,
"cdna_end": null,
"cdna_length": 3968,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPPR5",
"gene_hgnc_id": 31703,
"hgvs_c": "c.435C>T",
"hgvs_p": "p.Val145Val",
"transcript": "ENST00000696571.1",
"protein_id": "ENSP00000512726.1",
"transcript_support_level": null,
"aa_start": 145,
"aa_end": null,
"aa_length": 261,
"cds_start": 435,
"cds_end": null,
"cds_length": 786,
"cdna_start": 523,
"cdna_end": null,
"cdna_length": 3701,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPPR5",
"gene_hgnc_id": 31703,
"hgvs_c": "c.552C>T",
"hgvs_p": "p.Val184Val",
"transcript": "XM_011540838.4",
"protein_id": "XP_011539140.1",
"transcript_support_level": null,
"aa_start": 184,
"aa_end": null,
"aa_length": 305,
"cds_start": 552,
"cds_end": null,
"cds_length": 918,
"cdna_start": 1233,
"cdna_end": null,
"cdna_length": 4426,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PLPPR5",
"gene_hgnc_id": 31703,
"dbsnp": "rs309087",
"frequency_reference_population": 6.841087e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84109e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.38999998569488525,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.586,
"phylop100way_prediction": "Benign",
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP7",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 3,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000263177.5",
"gene_symbol": "PLPPR5",
"hgnc_id": 31703,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.600C>T",
"hgvs_p": "p.Val200Val"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}