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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: 8-64596687-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=64596687&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"BP4_Strong",
"BP6",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "CYP7B1",
"hgnc_id": 2652,
"hgvs_c": "c.1476G>A",
"hgvs_p": "p.Gln492Gln",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -6,
"transcript": "NM_004820.5",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP6,BP7",
"acmg_score": -6,
"allele_count_reference_population": 17,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.78,
"chr": "8",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "CYP7B1-related disorder,Spastic paraplegia,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.7799999713897705,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 506,
"aa_ref": "Q",
"aa_start": 492,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7462,
"cdna_start": 1626,
"cds_end": null,
"cds_length": 1521,
"cds_start": 1476,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_004820.5",
"gene_hgnc_id": 2652,
"gene_symbol": "CYP7B1",
"hgvs_c": "c.1476G>A",
"hgvs_p": "p.Gln492Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000310193.4",
"protein_coding": true,
"protein_id": "NP_004811.1",
"strand": false,
"transcript": "NM_004820.5",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 506,
"aa_ref": "Q",
"aa_start": 492,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 7462,
"cdna_start": 1626,
"cds_end": null,
"cds_length": 1521,
"cds_start": 1476,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000310193.4",
"gene_hgnc_id": 2652,
"gene_symbol": "CYP7B1",
"hgvs_c": "c.1476G>A",
"hgvs_p": "p.Gln492Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004820.5",
"protein_coding": true,
"protein_id": "ENSP00000310721.3",
"strand": false,
"transcript": "ENST00000310193.4",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 557,
"aa_ref": "Q",
"aa_start": 543,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2134,
"cdna_start": 1779,
"cds_end": null,
"cds_length": 1674,
"cds_start": 1629,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000864436.1",
"gene_hgnc_id": 2652,
"gene_symbol": "CYP7B1",
"hgvs_c": "c.1629G>A",
"hgvs_p": "p.Gln543Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534495.1",
"strand": false,
"transcript": "ENST00000864436.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 506,
"aa_ref": "Q",
"aa_start": 492,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1813,
"cdna_start": 1743,
"cds_end": null,
"cds_length": 1521,
"cds_start": 1476,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000864435.1",
"gene_hgnc_id": 2652,
"gene_symbol": "CYP7B1",
"hgvs_c": "c.1476G>A",
"hgvs_p": "p.Gln492Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534494.1",
"strand": false,
"transcript": "ENST00000864435.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 437,
"aa_ref": "Q",
"aa_start": 423,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1503,
"cdna_start": 1419,
"cds_end": null,
"cds_length": 1314,
"cds_start": 1269,
"consequences": [
"synonymous_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000948771.1",
"gene_hgnc_id": 2652,
"gene_symbol": "CYP7B1",
"hgvs_c": "c.1269G>A",
"hgvs_p": "p.Gln423Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000618830.1",
"strand": false,
"transcript": "ENST00000948771.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 528,
"aa_ref": "Q",
"aa_start": 514,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 25913,
"cdna_start": 20077,
"cds_end": null,
"cds_length": 1587,
"cds_start": 1542,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_017014002.2",
"gene_hgnc_id": 2652,
"gene_symbol": "CYP7B1",
"hgvs_c": "c.1542G>A",
"hgvs_p": "p.Gln514Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016869491.1",
"strand": false,
"transcript": "XM_017014002.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 460,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2651,
"cdna_start": null,
"cds_end": null,
"cds_length": 1383,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001324112.2",
"gene_hgnc_id": 2652,
"gene_symbol": "CYP7B1",
"hgvs_c": "c.1234-6843G>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001311041.1",
"strand": false,
"transcript": "NM_001324112.2",
"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": 587,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000523954.1",
"gene_hgnc_id": 2652,
"gene_symbol": "CYP7B1",
"hgvs_c": "n.508-6843G>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000523954.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs372800597",
"effect": "synonymous_variant",
"frequency_reference_population": 0.000010536206,
"gene_hgnc_id": 2652,
"gene_symbol": "CYP7B1",
"gnomad_exomes_ac": 8,
"gnomad_exomes_af": 0.00000547503,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 9,
"gnomad_genomes_af": 0.0000590923,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not provided|Spastic paraplegia|CYP7B1-related disorder",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.715,
"pos": 64596687,
"ref": "C",
"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_004820.5"
}
]
}