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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: 6-1390035-CCGCCGCCCGCCGCCG-CCGCCGC (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=1390035&ref=CCGCCGCCCGCCGCCG&alt=CCGCCGC&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 5,
"criteria": [
"BP6",
"BS2"
],
"effects": [
"conservative_inframe_deletion"
],
"gene_symbol": "FOXF2",
"hgnc_id": 3810,
"hgvs_c": "c.115_123delGCCGCCGCC",
"hgvs_p": "p.Ala39_Ala41del",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -5,
"transcript": "NM_001452.2",
"verdict": "Likely_benign"
},
{
"benign_score": 1,
"criteria": [
"BP6"
],
"effects": [
"intron_variant"
],
"gene_symbol": "FOXF2-DT",
"hgnc_id": 50662,
"hgvs_c": "n.458+32_458+40delCGGCGGCGG",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -1,
"transcript": "NR_189293.1",
"verdict": "Likely_benign"
},
{
"benign_score": 1,
"criteria": [
"BP6"
],
"effects": [
"intron_variant"
],
"gene_symbol": "LINC01394",
"hgnc_id": 50670,
"hgvs_c": "n.89+942_89+950delCGGCGGCGG",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -1,
"transcript": "ENST00000721686.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP6,BS2",
"acmg_score": -5,
"allele_count_reference_population": 1075,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "6",
"clinvar_classification": "Likely benign",
"clinvar_disease": "FOXF2-related disorder",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 444,
"aa_ref": "AAA",
"aa_start": 39,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2451,
"cdna_start": 487,
"cds_end": null,
"cds_length": 1335,
"cds_start": 115,
"consequences": [
"conservative_inframe_deletion"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001452.2",
"gene_hgnc_id": 3810,
"gene_symbol": "FOXF2",
"hgvs_c": "c.115_123delGCCGCCGCC",
"hgvs_p": "p.Ala39_Ala41del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000645481.2",
"protein_coding": true,
"protein_id": "NP_001443.1",
"strand": true,
"transcript": "NM_001452.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 444,
"aa_ref": "AAA",
"aa_start": 39,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2451,
"cdna_start": 487,
"cds_end": null,
"cds_length": 1335,
"cds_start": 115,
"consequences": [
"conservative_inframe_deletion"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000645481.2",
"gene_hgnc_id": 3810,
"gene_symbol": "FOXF2",
"hgvs_c": "c.115_123delGCCGCCGCC",
"hgvs_p": "p.Ala39_Ala41del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001452.2",
"protein_coding": true,
"protein_id": "ENSP00000496415.1",
"strand": true,
"transcript": "ENST00000645481.2",
"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": 998,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000721686.1",
"gene_hgnc_id": 50670,
"gene_symbol": "LINC01394",
"hgvs_c": "n.89+942_89+950delCGGCGGCGG",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000721686.1",
"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": 1185,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000721687.1",
"gene_hgnc_id": 50670,
"gene_symbol": "LINC01394",
"hgvs_c": "n.69-824_69-816delCGGCGGCGG",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000721687.1",
"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": 2375,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_189293.1",
"gene_hgnc_id": 50662,
"gene_symbol": "FOXF2-DT",
"hgvs_c": "n.458+32_458+40delCGGCGGCGG",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_189293.1",
"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": 1985,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_189294.1",
"gene_hgnc_id": 50662,
"gene_symbol": "FOXF2-DT",
"hgvs_c": "n.69-824_69-816delCGGCGGCGG",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_189294.1",
"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": 1777,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_189295.1",
"gene_hgnc_id": 50662,
"gene_symbol": "FOXF2-DT",
"hgvs_c": "n.68+942_68+950delCGGCGGCGG",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_189295.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs747033801",
"effect": "conservative_inframe_deletion",
"frequency_reference_population": 0.00079358637,
"gene_hgnc_id": 3810,
"gene_symbol": "FOXF2",
"gnomad_exomes_ac": 830,
"gnomad_exomes_af": 0.000686337,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 245,
"gnomad_genomes_af": 0.00168626,
"gnomad_genomes_homalt": 1,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 2,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "FOXF2-related disorder",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.309,
"pos": 1390041,
"ref": "CCCGCCGCCG",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": null,
"splice_score_selected": null,
"splice_source_selected": null,
"spliceai_max_prediction": null,
"spliceai_max_score": null,
"transcript": "NM_001452.2"
}
]
}