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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-133536135-GGAA-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=133536135&ref=GGAA&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PM4_Supporting"
],
"effects": [
"conservative_inframe_deletion"
],
"gene_symbol": "GPC3",
"hgnc_id": 4451,
"hgvs_c": "c.1798_1800delTTC",
"hgvs_p": "p.Phe600del",
"inheritance_mode": "XL",
"pathogenic_score": 3,
"score": 3,
"transcript": "NM_001164617.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PM4_Supporting",
"acmg_score": 3,
"allele_count_reference_population": 3,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "X",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Wilms tumor 1",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 580,
"aa_ref": "F",
"aa_start": 577,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2267,
"cdna_start": 1876,
"cds_end": null,
"cds_length": 1743,
"cds_start": 1729,
"consequences": [
"conservative_inframe_deletion"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_004484.4",
"gene_hgnc_id": 4451,
"gene_symbol": "GPC3",
"hgvs_c": "c.1729_1731delTTC",
"hgvs_p": "p.Phe577del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000370818.8",
"protein_coding": true,
"protein_id": "NP_004475.1",
"strand": false,
"transcript": "NM_004484.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 580,
"aa_ref": "F",
"aa_start": 577,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2267,
"cdna_start": 1876,
"cds_end": null,
"cds_length": 1743,
"cds_start": 1729,
"consequences": [
"conservative_inframe_deletion"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000370818.8",
"gene_hgnc_id": 4451,
"gene_symbol": "GPC3",
"hgvs_c": "c.1729_1731delTTC",
"hgvs_p": "p.Phe577del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004484.4",
"protein_coding": true,
"protein_id": "ENSP00000359854.3",
"strand": false,
"transcript": "ENST00000370818.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 603,
"aa_ref": "F",
"aa_start": 600,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2336,
"cdna_start": 1945,
"cds_end": null,
"cds_length": 1812,
"cds_start": 1798,
"consequences": [
"conservative_inframe_deletion"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000394299.7",
"gene_hgnc_id": 4451,
"gene_symbol": "GPC3",
"hgvs_c": "c.1798_1800delTTC",
"hgvs_p": "p.Phe600del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000377836.2",
"strand": false,
"transcript": "ENST00000394299.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 526,
"aa_ref": "F",
"aa_start": 523,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1581,
"cdna_start": 1569,
"cds_end": null,
"cds_length": 1581,
"cds_start": 1567,
"consequences": [
"conservative_inframe_deletion"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000631057.2",
"gene_hgnc_id": 4451,
"gene_symbol": "GPC3",
"hgvs_c": "c.1567_1569delTTC",
"hgvs_p": "p.Phe523del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000486325.1",
"strand": false,
"transcript": "ENST00000631057.2",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 616,
"aa_ref": "F",
"aa_start": 613,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2234,
"cdna_start": 1984,
"cds_end": null,
"cds_length": 1851,
"cds_start": 1837,
"consequences": [
"conservative_inframe_deletion"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000911059.1",
"gene_hgnc_id": 4451,
"gene_symbol": "GPC3",
"hgvs_c": "c.1837_1839delTTC",
"hgvs_p": "p.Phe613del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000581118.1",
"strand": false,
"transcript": "ENST00000911059.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 603,
"aa_ref": "F",
"aa_start": 600,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2336,
"cdna_start": 1945,
"cds_end": null,
"cds_length": 1812,
"cds_start": 1798,
"consequences": [
"conservative_inframe_deletion"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001164617.2",
"gene_hgnc_id": 4451,
"gene_symbol": "GPC3",
"hgvs_c": "c.1798_1800delTTC",
"hgvs_p": "p.Phe600del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001158089.1",
"strand": false,
"transcript": "NM_001164617.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 564,
"aa_ref": "F",
"aa_start": 561,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2219,
"cdna_start": 1828,
"cds_end": null,
"cds_length": 1695,
"cds_start": 1681,
"consequences": [
"conservative_inframe_deletion"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001164618.2",
"gene_hgnc_id": 4451,
"gene_symbol": "GPC3",
"hgvs_c": "c.1681_1683delTTC",
"hgvs_p": "p.Phe561del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001158090.1",
"strand": false,
"transcript": "NM_001164618.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 564,
"aa_ref": "F",
"aa_start": 561,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1974,
"cdna_start": 1851,
"cds_end": null,
"cds_length": 1695,
"cds_start": 1681,
"consequences": [
"conservative_inframe_deletion"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000689310.1",
"gene_hgnc_id": 4451,
"gene_symbol": "GPC3",
"hgvs_c": "c.1681_1683delTTC",
"hgvs_p": "p.Phe561del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000510438.1",
"strand": false,
"transcript": "ENST00000689310.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 538,
"aa_ref": "F",
"aa_start": 535,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2139,
"cdna_start": 1750,
"cds_end": null,
"cds_length": 1617,
"cds_start": 1603,
"consequences": [
"conservative_inframe_deletion"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000925127.1",
"gene_hgnc_id": 4451,
"gene_symbol": "GPC3",
"hgvs_c": "c.1603_1605delTTC",
"hgvs_p": "p.Phe535del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595186.1",
"strand": false,
"transcript": "ENST00000925127.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 526,
"aa_ref": "F",
"aa_start": 523,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2105,
"cdna_start": 1714,
"cds_end": null,
"cds_length": 1581,
"cds_start": 1567,
"consequences": [
"conservative_inframe_deletion"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001164619.2",
"gene_hgnc_id": 4451,
"gene_symbol": "GPC3",
"hgvs_c": "c.1567_1569delTTC",
"hgvs_p": "p.Phe523del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001158091.1",
"strand": false,
"transcript": "NM_001164619.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 453,
"aa_ref": "F",
"aa_start": 450,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2229,
"cdna_start": 1838,
"cds_end": null,
"cds_length": 1362,
"cds_start": 1348,
"consequences": [
"conservative_inframe_deletion"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000925126.1",
"gene_hgnc_id": 4451,
"gene_symbol": "GPC3",
"hgvs_c": "c.1348_1350delTTC",
"hgvs_p": "p.Phe450del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595185.1",
"strand": false,
"transcript": "ENST00000925126.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 342,
"aa_ref": "F",
"aa_start": 339,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1030,
"cdna_start": 1018,
"cds_end": null,
"cds_length": 1029,
"cds_start": 1015,
"consequences": [
"conservative_inframe_deletion"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000692084.1",
"gene_hgnc_id": 4451,
"gene_symbol": "GPC3",
"hgvs_c": "c.1015_1017delTTC",
"hgvs_p": "p.Phe339del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000508554.1",
"strand": false,
"transcript": "ENST00000692084.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 309,
"aa_ref": "F",
"aa_start": 306,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 932,
"cdna_start": 920,
"cds_end": null,
"cds_length": 930,
"cds_start": 916,
"consequences": [
"conservative_inframe_deletion"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000406757.3",
"gene_hgnc_id": 4451,
"gene_symbol": "GPC3",
"hgvs_c": "c.916_918delTTC",
"hgvs_p": "p.Phe306del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000385307.3",
"strand": false,
"transcript": "ENST00000406757.3",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 761,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000666673.2",
"gene_hgnc_id": 4451,
"gene_symbol": "GPC3",
"hgvs_c": "n.760_*1delTTC",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000666673.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1188,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000669691.1",
"gene_hgnc_id": 4451,
"gene_symbol": "GPC3",
"hgvs_c": "n.795_797delTTC",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000669691.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 674,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000692074.1",
"gene_hgnc_id": 4451,
"gene_symbol": "GPC3",
"hgvs_c": "n.673_*1delTTC",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000692074.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 596,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000666017.1",
"gene_hgnc_id": 4451,
"gene_symbol": "GPC3",
"hgvs_c": "n.*11_*13delTTC",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000666017.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 761,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000666673.2",
"gene_hgnc_id": 4451,
"gene_symbol": "GPC3",
"hgvs_c": "n.760_*1delTTC",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000666673.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 785,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000667662.1",
"gene_hgnc_id": 4451,
"gene_symbol": "GPC3",
"hgvs_c": "n.*11_*13delTTC",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000667662.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 674,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000692074.1",
"gene_hgnc_id": 4451,
"gene_symbol": "GPC3",
"hgvs_c": "n.673_*1delTTC",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000692074.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1269354535",
"effect": "conservative_inframe_deletion",
"frequency_reference_population": 0.000002746795,
"gene_hgnc_id": 4451,
"gene_symbol": "GPC3",
"gnomad_exomes_ac": 3,
"gnomad_exomes_af": 0.00000274679,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Wilms tumor 1",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.37,
"pos": 133536135,
"ref": "GGAA",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001164617.2"
}
]
}