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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-133536151-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=133536151&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 133536151,
"ref": "C",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "ENST00000370818.8",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "V",
"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.1716G>C",
"hgvs_p": "p.Val572Val",
"transcript": "NM_004484.4",
"protein_id": "NP_004475.1",
"transcript_support_level": null,
"aa_start": 572,
"aa_end": null,
"aa_length": 580,
"cds_start": 1716,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1861,
"cdna_end": null,
"cdna_length": 2267,
"mane_select": "ENST00000370818.8",
"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": 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.1716G>C",
"hgvs_p": "p.Val572Val",
"transcript": "ENST00000370818.8",
"protein_id": "ENSP00000359854.3",
"transcript_support_level": 1,
"aa_start": 572,
"aa_end": null,
"aa_length": 580,
"cds_start": 1716,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1861,
"cdna_end": null,
"cdna_length": 2267,
"mane_select": "NM_004484.4",
"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": 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.1785G>C",
"hgvs_p": "p.Val595Val",
"transcript": "ENST00000394299.7",
"protein_id": "ENSP00000377836.2",
"transcript_support_level": 1,
"aa_start": 595,
"aa_end": null,
"aa_length": 603,
"cds_start": 1785,
"cds_end": null,
"cds_length": 1812,
"cdna_start": 1930,
"cdna_end": null,
"cdna_length": 2336,
"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": 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.1554G>C",
"hgvs_p": "p.Val518Val",
"transcript": "ENST00000631057.2",
"protein_id": "ENSP00000486325.1",
"transcript_support_level": 1,
"aa_start": 518,
"aa_end": null,
"aa_length": 526,
"cds_start": 1554,
"cds_end": null,
"cds_length": 1581,
"cdna_start": 1554,
"cdna_end": null,
"cdna_length": 1581,
"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": 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.1785G>C",
"hgvs_p": "p.Val595Val",
"transcript": "NM_001164617.2",
"protein_id": "NP_001158089.1",
"transcript_support_level": null,
"aa_start": 595,
"aa_end": null,
"aa_length": 603,
"cds_start": 1785,
"cds_end": null,
"cds_length": 1812,
"cdna_start": 1930,
"cdna_end": null,
"cdna_length": 2336,
"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": 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.1668G>C",
"hgvs_p": "p.Val556Val",
"transcript": "NM_001164618.2",
"protein_id": "NP_001158090.1",
"transcript_support_level": null,
"aa_start": 556,
"aa_end": null,
"aa_length": 564,
"cds_start": 1668,
"cds_end": null,
"cds_length": 1695,
"cdna_start": 1813,
"cdna_end": null,
"cdna_length": 2219,
"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": 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.1668G>C",
"hgvs_p": "p.Val556Val",
"transcript": "ENST00000689310.1",
"protein_id": "ENSP00000510438.1",
"transcript_support_level": null,
"aa_start": 556,
"aa_end": null,
"aa_length": 564,
"cds_start": 1668,
"cds_end": null,
"cds_length": 1695,
"cdna_start": 1836,
"cdna_end": null,
"cdna_length": 1974,
"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": 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.1554G>C",
"hgvs_p": "p.Val518Val",
"transcript": "NM_001164619.2",
"protein_id": "NP_001158091.1",
"transcript_support_level": null,
"aa_start": 518,
"aa_end": null,
"aa_length": 526,
"cds_start": 1554,
"cds_end": null,
"cds_length": 1581,
"cdna_start": 1699,
"cdna_end": null,
"cdna_length": 2105,
"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": 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.1002G>C",
"hgvs_p": "p.Val334Val",
"transcript": "ENST00000692084.1",
"protein_id": "ENSP00000508554.1",
"transcript_support_level": null,
"aa_start": 334,
"aa_end": null,
"aa_length": 342,
"cds_start": 1002,
"cds_end": null,
"cds_length": 1029,
"cdna_start": 1003,
"cdna_end": null,
"cdna_length": 1030,
"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": 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.903G>C",
"hgvs_p": "p.Val301Val",
"transcript": "ENST00000406757.3",
"protein_id": "ENSP00000385307.3",
"transcript_support_level": 2,
"aa_start": 301,
"aa_end": null,
"aa_length": 309,
"cds_start": 903,
"cds_end": null,
"cds_length": 930,
"cdna_start": 905,
"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": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "n.594G>C",
"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": 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.747G>C",
"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": false,
"consequences": [
"splice_region_variant",
"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.783G>C",
"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": 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.782G>C",
"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": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "n.660G>C",
"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": "rs779688123",
"frequency_reference_population": 0.00004231396,
"hom_count_reference_population": 18,
"allele_count_reference_population": 51,
"gnomad_exomes_af": 0.0000392741,
"gnomad_genomes_af": 0.0000724592,
"gnomad_exomes_ac": 43,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7799999713897705,
"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": -0.78,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.69,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000370818.8",
"gene_symbol": "GPC3",
"hgnc_id": 4451,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1716G>C",
"hgvs_p": "p.Val572Val"
}
],
"clinvar_disease": "Wilms tumor 1,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:1",
"phenotype_combined": "Wilms tumor 1|not specified",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}