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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: X-7077389-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=7077389&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 7077389,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001135565.2",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUDP",
"gene_hgnc_id": 16818,
"hgvs_c": "c.341G>T",
"hgvs_p": "p.Ser114Ile",
"transcript": "NM_012080.5",
"protein_id": "NP_036212.3",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 228,
"cds_start": 341,
"cds_end": null,
"cds_length": 687,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000381077.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_012080.5"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUDP",
"gene_hgnc_id": 16818,
"hgvs_c": "c.341G>T",
"hgvs_p": "p.Ser114Ile",
"transcript": "ENST00000381077.10",
"protein_id": "ENSP00000370467.6",
"transcript_support_level": 1,
"aa_start": 114,
"aa_end": null,
"aa_length": 228,
"cds_start": 341,
"cds_end": null,
"cds_length": 687,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_012080.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000381077.10"
},
{
"aa_ref": "S",
"aa_alt": "I",
"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": "PUDP",
"gene_hgnc_id": 16818,
"hgvs_c": "c.410G>T",
"hgvs_p": "p.Ser137Ile",
"transcript": "NM_001135565.2",
"protein_id": "NP_001129037.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 251,
"cds_start": 410,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001135565.2"
},
{
"aa_ref": "S",
"aa_alt": "I",
"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": "PUDP",
"gene_hgnc_id": 16818,
"hgvs_c": "c.410G>T",
"hgvs_p": "p.Ser137Ile",
"transcript": "ENST00000424830.6",
"protein_id": "ENSP00000396452.2",
"transcript_support_level": 3,
"aa_start": 137,
"aa_end": null,
"aa_length": 251,
"cds_start": 410,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000424830.6"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUDP",
"gene_hgnc_id": 16818,
"hgvs_c": "c.341G>T",
"hgvs_p": "p.Ser114Ile",
"transcript": "ENST00000934726.1",
"protein_id": "ENSP00000604785.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 238,
"cds_start": 341,
"cds_end": null,
"cds_length": 717,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934726.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUDP",
"gene_hgnc_id": 16818,
"hgvs_c": "c.341G>T",
"hgvs_p": "p.Ser114Ile",
"transcript": "NM_001178135.2",
"protein_id": "NP_001171606.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 208,
"cds_start": 341,
"cds_end": null,
"cds_length": 627,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001178135.2"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUDP",
"gene_hgnc_id": 16818,
"hgvs_c": "c.341G>T",
"hgvs_p": "p.Ser114Ile",
"transcript": "ENST00000486446.3",
"protein_id": "ENSP00000430995.2",
"transcript_support_level": 2,
"aa_start": 114,
"aa_end": null,
"aa_length": 208,
"cds_start": 341,
"cds_end": null,
"cds_length": 627,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000486446.3"
},
{
"aa_ref": "S",
"aa_alt": "I",
"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": "PUDP",
"gene_hgnc_id": 16818,
"hgvs_c": "c.281G>T",
"hgvs_p": "p.Ser94Ile",
"transcript": "ENST00000962956.1",
"protein_id": "ENSP00000633015.1",
"transcript_support_level": null,
"aa_start": 94,
"aa_end": null,
"aa_length": 208,
"cds_start": 281,
"cds_end": null,
"cds_length": 627,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962956.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUDP",
"gene_hgnc_id": 16818,
"hgvs_c": "c.212G>T",
"hgvs_p": "p.Ser71Ile",
"transcript": "NM_001178136.2",
"protein_id": "NP_001171607.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 185,
"cds_start": 212,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001178136.2"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUDP",
"gene_hgnc_id": 16818,
"hgvs_c": "c.212G>T",
"hgvs_p": "p.Ser71Ile",
"transcript": "ENST00000412827.6",
"protein_id": "ENSP00000406260.2",
"transcript_support_level": 2,
"aa_start": 71,
"aa_end": null,
"aa_length": 185,
"cds_start": 212,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000412827.6"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUDP",
"gene_hgnc_id": 16818,
"hgvs_c": "c.122G>T",
"hgvs_p": "p.Ser41Ile",
"transcript": "ENST00000870960.1",
"protein_id": "ENSP00000541019.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 155,
"cds_start": 122,
"cds_end": null,
"cds_length": 468,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870960.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUDP",
"gene_hgnc_id": 16818,
"hgvs_c": "n.35G>T",
"hgvs_p": null,
"transcript": "ENST00000655425.1",
"protein_id": "ENSP00000499460.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000655425.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUDP",
"gene_hgnc_id": 16818,
"hgvs_c": "n.381G>T",
"hgvs_p": null,
"transcript": "XR_001755734.2",
"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": "XR_001755734.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUDP",
"gene_hgnc_id": 16818,
"hgvs_c": "n.381G>T",
"hgvs_p": null,
"transcript": "XR_007068202.1",
"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": "XR_007068202.1"
}
],
"gene_symbol": "PUDP",
"gene_hgnc_id": 16818,
"dbsnp": null,
"frequency_reference_population": 9.1095507e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 9.10955e-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": 0.9270344376564026,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.481,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9812,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.13,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 6.59,
"phylop100way_prediction": "Uncertain_significance",
"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": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001135565.2",
"gene_symbol": "PUDP",
"hgnc_id": 16818,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.410G>T",
"hgvs_p": "p.Ser137Ile"
}
],
"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
}