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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: 8-51483681-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=51483681&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 51483681,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000356297.5",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDNL",
"gene_hgnc_id": 26359,
"hgvs_c": "c.486A>G",
"hgvs_p": "p.Pro162Pro",
"transcript": "NM_144651.5",
"protein_id": "NP_653252.4",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 1463,
"cds_start": 486,
"cds_end": null,
"cds_length": 4392,
"cdna_start": 587,
"cdna_end": null,
"cdna_length": 4807,
"mane_select": "ENST00000356297.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDNL",
"gene_hgnc_id": 26359,
"hgvs_c": "c.486A>G",
"hgvs_p": "p.Pro162Pro",
"transcript": "ENST00000356297.5",
"protein_id": "ENSP00000348645.4",
"transcript_support_level": 1,
"aa_start": 162,
"aa_end": null,
"aa_length": 1463,
"cds_start": 486,
"cds_end": null,
"cds_length": 4392,
"cdna_start": 587,
"cdna_end": null,
"cdna_length": 4807,
"mane_select": "NM_144651.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDNL",
"gene_hgnc_id": 26359,
"hgvs_c": "c.414A>G",
"hgvs_p": "p.Pro138Pro",
"transcript": "XM_047421364.1",
"protein_id": "XP_047277320.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 1439,
"cds_start": 414,
"cds_end": null,
"cds_length": 4320,
"cdna_start": 515,
"cdna_end": null,
"cdna_length": 4735,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDNL",
"gene_hgnc_id": 26359,
"hgvs_c": "c.414A>G",
"hgvs_p": "p.Pro138Pro",
"transcript": "XM_047421365.1",
"protein_id": "XP_047277321.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 1439,
"cds_start": 414,
"cds_end": null,
"cds_length": 4320,
"cdna_start": 515,
"cdna_end": null,
"cdna_length": 4735,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDNL",
"gene_hgnc_id": 26359,
"hgvs_c": "c.486A>G",
"hgvs_p": "p.Pro162Pro",
"transcript": "XM_047421366.1",
"protein_id": "XP_047277322.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 1367,
"cds_start": 486,
"cds_end": null,
"cds_length": 4104,
"cdna_start": 587,
"cdna_end": null,
"cdna_length": 4519,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDNL",
"gene_hgnc_id": 26359,
"hgvs_c": "c.81A>G",
"hgvs_p": "p.Pro27Pro",
"transcript": "XM_011517458.3",
"protein_id": "XP_011515760.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 1328,
"cds_start": 81,
"cds_end": null,
"cds_length": 3987,
"cdna_start": 261,
"cdna_end": null,
"cdna_length": 4481,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDNL",
"gene_hgnc_id": 26359,
"hgvs_c": "c.81A>G",
"hgvs_p": "p.Pro27Pro",
"transcript": "XM_017013041.2",
"protein_id": "XP_016868530.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 1328,
"cds_start": 81,
"cds_end": null,
"cds_length": 3987,
"cdna_start": 224,
"cdna_end": null,
"cdna_length": 4444,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDNL",
"gene_hgnc_id": 26359,
"hgvs_c": "c.81A>G",
"hgvs_p": "p.Pro27Pro",
"transcript": "XM_047421367.1",
"protein_id": "XP_047277323.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 1328,
"cds_start": 81,
"cds_end": null,
"cds_length": 3987,
"cdna_start": 750,
"cdna_end": null,
"cdna_length": 4970,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDNL",
"gene_hgnc_id": 26359,
"hgvs_c": "c.486A>G",
"hgvs_p": "p.Pro162Pro",
"transcript": "XM_047421369.1",
"protein_id": "XP_047277325.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 757,
"cds_start": 486,
"cds_end": null,
"cds_length": 2274,
"cdna_start": 587,
"cdna_end": null,
"cdna_length": 2755,
"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": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDNL",
"gene_hgnc_id": 26359,
"hgvs_c": "n.587A>G",
"hgvs_p": null,
"transcript": "XR_007060701.1",
"protein_id": null,
"transcript_support_level": null,
"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": 4562,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PXDNL",
"gene_hgnc_id": 26359,
"dbsnp": "rs7837348",
"frequency_reference_population": 0.17117359,
"hom_count_reference_population": 25352,
"allele_count_reference_population": 258582,
"gnomad_exomes_af": 0.163839,
"gnomad_genomes_af": 0.23667,
"gnomad_exomes_ac": 222576,
"gnomad_genomes_ac": 36006,
"gnomad_exomes_homalt": 20207,
"gnomad_genomes_homalt": 5145,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9200000166893005,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.05999999865889549,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.92,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.476,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.06,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000356297.5",
"gene_symbol": "PXDNL",
"hgnc_id": 26359,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.486A>G",
"hgvs_p": "p.Pro162Pro"
}
],
"clinvar_disease": "PXDNL-related disorder,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not specified|PXDNL-related disorder|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}