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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-133953138-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=133953138&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 133953138,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000370818.8",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "c.249A>G",
"hgvs_p": "p.Leu83Leu",
"transcript": "NM_004484.4",
"protein_id": "NP_004475.1",
"transcript_support_level": null,
"aa_start": 83,
"aa_end": null,
"aa_length": 580,
"cds_start": 249,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 394,
"cdna_end": null,
"cdna_length": 2267,
"mane_select": "ENST00000370818.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "c.249A>G",
"hgvs_p": "p.Leu83Leu",
"transcript": "ENST00000370818.8",
"protein_id": "ENSP00000359854.3",
"transcript_support_level": 1,
"aa_start": 83,
"aa_end": null,
"aa_length": 580,
"cds_start": 249,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 394,
"cdna_end": null,
"cdna_length": 2267,
"mane_select": "NM_004484.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "c.249A>G",
"hgvs_p": "p.Leu83Leu",
"transcript": "ENST00000394299.7",
"protein_id": "ENSP00000377836.2",
"transcript_support_level": 1,
"aa_start": 83,
"aa_end": null,
"aa_length": 603,
"cds_start": 249,
"cds_end": null,
"cds_length": 1812,
"cdna_start": 394,
"cdna_end": null,
"cdna_length": 2336,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "c.175+32137A>G",
"hgvs_p": null,
"transcript": "ENST00000631057.2",
"protein_id": "ENSP00000486325.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 526,
"cds_start": -4,
"cds_end": null,
"cds_length": 1581,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "c.249A>G",
"hgvs_p": "p.Leu83Leu",
"transcript": "NM_001164617.2",
"protein_id": "NP_001158089.1",
"transcript_support_level": null,
"aa_start": 83,
"aa_end": null,
"aa_length": 603,
"cds_start": 249,
"cds_end": null,
"cds_length": 1812,
"cdna_start": 394,
"cdna_end": null,
"cdna_length": 2336,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "c.249A>G",
"hgvs_p": "p.Leu83Leu",
"transcript": "NM_001164618.2",
"protein_id": "NP_001158090.1",
"transcript_support_level": null,
"aa_start": 83,
"aa_end": null,
"aa_length": 564,
"cds_start": 249,
"cds_end": null,
"cds_length": 1695,
"cdna_start": 394,
"cdna_end": null,
"cdna_length": 2219,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "c.249A>G",
"hgvs_p": "p.Leu83Leu",
"transcript": "ENST00000689310.1",
"protein_id": "ENSP00000510438.1",
"transcript_support_level": null,
"aa_start": 83,
"aa_end": null,
"aa_length": 564,
"cds_start": 249,
"cds_end": null,
"cds_length": 1695,
"cdna_start": 417,
"cdna_end": null,
"cdna_length": 1974,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "c.249A>G",
"hgvs_p": "p.Leu83Leu",
"transcript": "XM_017029413.3",
"protein_id": "XP_016884902.1",
"transcript_support_level": null,
"aa_start": 83,
"aa_end": null,
"aa_length": 486,
"cds_start": 249,
"cds_end": null,
"cds_length": 1461,
"cdna_start": 394,
"cdna_end": null,
"cdna_length": 1621,
"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": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "n.249A>G",
"hgvs_p": null,
"transcript": "ENST00000684880.1",
"protein_id": "ENSP00000510280.1",
"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": 1764,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "n.379A>G",
"hgvs_p": null,
"transcript": "ENST00000692630.1",
"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": 600,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"hgvs_c": "c.175+32137A>G",
"hgvs_p": null,
"transcript": "NM_001164619.2",
"protein_id": "NP_001158091.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 526,
"cds_start": -4,
"cds_end": null,
"cds_length": 1581,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2105,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GPC3",
"gene_hgnc_id": 4451,
"dbsnp": "rs755510528",
"frequency_reference_population": 0.000009150487,
"hom_count_reference_population": 4,
"allele_count_reference_population": 10,
"gnomad_exomes_af": 0.00000915049,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 10,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6299999952316284,
"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": -0.63,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.82,
"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": -17,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS2",
"acmg_by_gene": [
{
"score": -17,
"benign_score": 17,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000370818.8",
"gene_symbol": "GPC3",
"hgnc_id": 4451,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.249A>G",
"hgvs_p": "p.Leu83Leu"
}
],
"clinvar_disease": "Wilms tumor 1,not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "Wilms tumor 1|not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}