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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: 19-13906456-AGGACCCCCG-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=13906456&ref=AGGACCCCCG&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 13906456,
"ref": "AGGACCCCCG",
"alt": "A",
"effect": "disruptive_inframe_deletion",
"transcript": "NM_017721.5",
"consequences": [
{
"aa_ref": "GPPG",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D1A",
"gene_hgnc_id": 30237,
"hgvs_c": "c.27_35delACCCCCGGG",
"hgvs_p": "p.Pro10_Gly12del",
"transcript": "NM_017721.5",
"protein_id": "NP_060191.3",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 951,
"cds_start": 27,
"cds_end": null,
"cds_length": 2856,
"cdna_start": 268,
"cdna_end": null,
"cdna_length": 3581,
"mane_select": "ENST00000318003.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "GPPG",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D1A",
"gene_hgnc_id": 30237,
"hgvs_c": "c.27_35delACCCCCGGG",
"hgvs_p": "p.Pro10_Gly12del",
"transcript": "ENST00000318003.11",
"protein_id": "ENSP00000313601.6",
"transcript_support_level": 1,
"aa_start": 9,
"aa_end": null,
"aa_length": 951,
"cds_start": 27,
"cds_end": null,
"cds_length": 2856,
"cdna_start": 268,
"cdna_end": null,
"cdna_length": 3581,
"mane_select": "NM_017721.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "GPPG",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D1A",
"gene_hgnc_id": 30237,
"hgvs_c": "c.27_35delACCCCCGGG",
"hgvs_p": "p.Pro10_Gly12del",
"transcript": "ENST00000589606.5",
"protein_id": "ENSP00000467526.1",
"transcript_support_level": 1,
"aa_start": 9,
"aa_end": null,
"aa_length": 950,
"cds_start": 27,
"cds_end": null,
"cds_length": 2853,
"cdna_start": 27,
"cdna_end": null,
"cdna_length": 3117,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "GPPG",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D1A",
"gene_hgnc_id": 30237,
"hgvs_c": "c.27_35delACCCCCGGG",
"hgvs_p": "p.Pro10_Gly12del",
"transcript": "NM_001411138.1",
"protein_id": "NP_001398067.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 950,
"cds_start": 27,
"cds_end": null,
"cds_length": 2853,
"cdna_start": 268,
"cdna_end": null,
"cdna_length": 3578,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "GPPG",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D1A",
"gene_hgnc_id": 30237,
"hgvs_c": "c.27_35delACCCCCGGG",
"hgvs_p": "p.Pro10_Gly12del",
"transcript": "XM_047439012.1",
"protein_id": "XP_047294968.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 950,
"cds_start": 27,
"cds_end": null,
"cds_length": 2853,
"cdna_start": 268,
"cdna_end": null,
"cdna_length": 3578,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "GPPG",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D1A",
"gene_hgnc_id": 30237,
"hgvs_c": "c.27_35delACCCCCGGG",
"hgvs_p": "p.Pro10_Gly12del",
"transcript": "XM_047439014.1",
"protein_id": "XP_047294970.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 949,
"cds_start": 27,
"cds_end": null,
"cds_length": 2850,
"cdna_start": 268,
"cdna_end": null,
"cdna_length": 3575,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "GPPG",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D1A",
"gene_hgnc_id": 30237,
"hgvs_c": "c.27_35delACCCCCGGG",
"hgvs_p": "p.Pro10_Gly12del",
"transcript": "XM_047439015.1",
"protein_id": "XP_047294971.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 947,
"cds_start": 27,
"cds_end": null,
"cds_length": 2844,
"cdna_start": 268,
"cdna_end": null,
"cdna_length": 3569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "GPPG",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D1A",
"gene_hgnc_id": 30237,
"hgvs_c": "c.27_35delACCCCCGGG",
"hgvs_p": "p.Pro10_Gly12del",
"transcript": "XM_047439016.1",
"protein_id": "XP_047294972.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 946,
"cds_start": 27,
"cds_end": null,
"cds_length": 2841,
"cdna_start": 268,
"cdna_end": null,
"cdna_length": 3566,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "GPPG",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D1A",
"gene_hgnc_id": 30237,
"hgvs_c": "c.27_35delACCCCCGGG",
"hgvs_p": "p.Pro10_Gly12del",
"transcript": "XM_047439017.1",
"protein_id": "XP_047294973.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 946,
"cds_start": 27,
"cds_end": null,
"cds_length": 2841,
"cdna_start": 268,
"cdna_end": null,
"cdna_length": 3566,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "GPPG",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D1A",
"gene_hgnc_id": 30237,
"hgvs_c": "c.27_35delACCCCCGGG",
"hgvs_p": "p.Pro10_Gly12del",
"transcript": "XM_047439018.1",
"protein_id": "XP_047294974.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 945,
"cds_start": 27,
"cds_end": null,
"cds_length": 2838,
"cdna_start": 268,
"cdna_end": null,
"cdna_length": 3563,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D1A",
"gene_hgnc_id": 30237,
"hgvs_c": "n.266_274delACCCCCGGG",
"hgvs_p": null,
"transcript": "ENST00000585896.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 1843,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D1A",
"gene_hgnc_id": 30237,
"hgvs_c": "n.185_193delACCCCCGGG",
"hgvs_p": null,
"transcript": "ENST00000680439.1",
"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": 2163,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BRME1",
"gene_hgnc_id": 28153,
"hgvs_c": "c.-298_-290delCGGGGGTCC",
"hgvs_p": null,
"transcript": "ENST00000585755.1",
"protein_id": "ENSP00000466119.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 24,
"cds_start": -4,
"cds_end": null,
"cds_length": 75,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 360,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CC2D1A",
"gene_hgnc_id": 30237,
"dbsnp": "rs1028125077",
"frequency_reference_population": 0.000098866985,
"hom_count_reference_population": 0,
"allele_count_reference_population": 150,
"gnomad_exomes_af": 0.000103999,
"gnomad_genomes_af": 0.0000527044,
"gnomad_exomes_ac": 142,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 4.256,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM4",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_017721.5",
"gene_symbol": "CC2D1A",
"hgnc_id": 30237,
"effects": [
"disruptive_inframe_deletion"
],
"inheritance_mode": "AR",
"hgvs_c": "c.27_35delACCCCCGGG",
"hgvs_p": "p.Pro10_Gly12del"
},
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000585755.1",
"gene_symbol": "BRME1",
"hgnc_id": 28153,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.-298_-290delCGGGGGTCC",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal recessive 3,Intellectual disability,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "not provided|Intellectual disability, autosomal recessive 3",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}