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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-133536136-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=133536136&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 133536136,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_004484.4",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "c.1731C>T",
"hgvs_p": "p.Phe577Phe",
"transcript": "NM_004484.4",
"protein_id": "NP_004475.1",
"transcript_support_level": null,
"aa_start": 577,
"aa_end": null,
"aa_length": 580,
"cds_start": 1731,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1876,
"cdna_end": null,
"cdna_length": 2267,
"mane_select": "ENST00000370818.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "c.1731C>T",
"hgvs_p": "p.Phe577Phe",
"transcript": "ENST00000370818.8",
"protein_id": "ENSP00000359854.3",
"transcript_support_level": 1,
"aa_start": 577,
"aa_end": null,
"aa_length": 580,
"cds_start": 1731,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1876,
"cdna_end": null,
"cdna_length": 2267,
"mane_select": "NM_004484.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "c.1800C>T",
"hgvs_p": "p.Phe600Phe",
"transcript": "ENST00000394299.7",
"protein_id": "ENSP00000377836.2",
"transcript_support_level": 1,
"aa_start": 600,
"aa_end": null,
"aa_length": 603,
"cds_start": 1800,
"cds_end": null,
"cds_length": 1812,
"cdna_start": 1945,
"cdna_end": null,
"cdna_length": 2336,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "c.1569C>T",
"hgvs_p": "p.Phe523Phe",
"transcript": "ENST00000631057.2",
"protein_id": "ENSP00000486325.1",
"transcript_support_level": 1,
"aa_start": 523,
"aa_end": null,
"aa_length": 526,
"cds_start": 1569,
"cds_end": null,
"cds_length": 1581,
"cdna_start": 1569,
"cdna_end": null,
"cdna_length": 1581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "c.1800C>T",
"hgvs_p": "p.Phe600Phe",
"transcript": "NM_001164617.2",
"protein_id": "NP_001158089.1",
"transcript_support_level": null,
"aa_start": 600,
"aa_end": null,
"aa_length": 603,
"cds_start": 1800,
"cds_end": null,
"cds_length": 1812,
"cdna_start": 1945,
"cdna_end": null,
"cdna_length": 2336,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "c.1683C>T",
"hgvs_p": "p.Phe561Phe",
"transcript": "NM_001164618.2",
"protein_id": "NP_001158090.1",
"transcript_support_level": null,
"aa_start": 561,
"aa_end": null,
"aa_length": 564,
"cds_start": 1683,
"cds_end": null,
"cds_length": 1695,
"cdna_start": 1828,
"cdna_end": null,
"cdna_length": 2219,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "c.1683C>T",
"hgvs_p": "p.Phe561Phe",
"transcript": "ENST00000689310.1",
"protein_id": "ENSP00000510438.1",
"transcript_support_level": null,
"aa_start": 561,
"aa_end": null,
"aa_length": 564,
"cds_start": 1683,
"cds_end": null,
"cds_length": 1695,
"cdna_start": 1851,
"cdna_end": null,
"cdna_length": 1974,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "c.1569C>T",
"hgvs_p": "p.Phe523Phe",
"transcript": "NM_001164619.2",
"protein_id": "NP_001158091.1",
"transcript_support_level": null,
"aa_start": 523,
"aa_end": null,
"aa_length": 526,
"cds_start": 1569,
"cds_end": null,
"cds_length": 1581,
"cdna_start": 1714,
"cdna_end": null,
"cdna_length": 2105,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "c.1017C>T",
"hgvs_p": "p.Phe339Phe",
"transcript": "ENST00000692084.1",
"protein_id": "ENSP00000508554.1",
"transcript_support_level": null,
"aa_start": 339,
"aa_end": null,
"aa_length": 342,
"cds_start": 1017,
"cds_end": null,
"cds_length": 1029,
"cdna_start": 1018,
"cdna_end": null,
"cdna_length": 1030,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "c.918C>T",
"hgvs_p": "p.Phe306Phe",
"transcript": "ENST00000406757.3",
"protein_id": "ENSP00000385307.3",
"transcript_support_level": 2,
"aa_start": 306,
"aa_end": null,
"aa_length": 309,
"cds_start": 918,
"cds_end": null,
"cds_length": 930,
"cdna_start": 920,
"cdna_end": null,
"cdna_length": 932,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "n.797C>T",
"hgvs_p": null,
"transcript": "ENST00000669691.1",
"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": 1188,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "n.*13C>T",
"hgvs_p": null,
"transcript": "ENST00000666017.1",
"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": 596,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "n.*1C>T",
"hgvs_p": null,
"transcript": "ENST00000666673.2",
"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": 761,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "n.*13C>T",
"hgvs_p": null,
"transcript": "ENST00000667662.1",
"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": 785,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "n.*1C>T",
"hgvs_p": null,
"transcript": "ENST00000692074.1",
"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": 674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"dbsnp": "rs745400193",
"frequency_reference_population": 0.0000018305061,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000183051,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.41999998688697815,
"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": -0.42,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.269,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_004484.4",
"gene_symbol": "GPC3",
"hgnc_id": 4451,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1731C>T",
"hgvs_p": "p.Phe577Phe"
}
],
"clinvar_disease": "Wilms tumor 1",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Wilms tumor 1",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}