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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: 11-77243815-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=77243815&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "GDPD4",
"hgnc_id": 24849,
"hgvs_c": "c.1120G>A",
"hgvs_p": "p.Val374Ile",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_182833.3",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_score": -4,
"allele_count_reference_population": 55,
"alphamissense_prediction": null,
"alphamissense_score": 0.1351,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.59,
"chr": "11",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.0511784553527832,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 520,
"aa_ref": "V",
"aa_start": 374,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2617,
"cdna_start": 1455,
"cds_end": null,
"cds_length": 1563,
"cds_start": 1120,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_182833.3",
"gene_hgnc_id": 24849,
"gene_symbol": "GDPD4",
"hgvs_c": "c.1120G>A",
"hgvs_p": "p.Val374Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000315938.5",
"protein_coding": true,
"protein_id": "NP_878253.1",
"strand": false,
"transcript": "NM_182833.3",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 520,
"aa_ref": "V",
"aa_start": 374,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2617,
"cdna_start": 1455,
"cds_end": null,
"cds_length": 1563,
"cds_start": 1120,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000315938.5",
"gene_hgnc_id": 24849,
"gene_symbol": "GDPD4",
"hgvs_c": "c.1120G>A",
"hgvs_p": "p.Val374Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_182833.3",
"protein_coding": true,
"protein_id": "ENSP00000320815.4",
"strand": false,
"transcript": "ENST00000315938.5",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 623,
"aa_ref": "V",
"aa_start": 374,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2502,
"cdna_start": 1371,
"cds_end": null,
"cds_length": 1872,
"cds_start": 1120,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000376217.6",
"gene_hgnc_id": 24849,
"gene_symbol": "GDPD4",
"hgvs_c": "c.1120G>A",
"hgvs_p": "p.Val374Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000365390.2",
"strand": false,
"transcript": "ENST00000376217.6",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 649,
"aa_ref": "V",
"aa_start": 400,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2728,
"cdna_start": 1597,
"cds_end": null,
"cds_length": 1950,
"cds_start": 1198,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "XM_011544834.1",
"gene_hgnc_id": 24849,
"gene_symbol": "GDPD4",
"hgvs_c": "c.1198G>A",
"hgvs_p": "p.Val400Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011543136.1",
"strand": false,
"transcript": "XM_011544834.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 322,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3915,
"cdna_start": null,
"cds_end": null,
"cds_length": 969,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 13,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047426557.1",
"gene_hgnc_id": 24849,
"gene_symbol": "GDPD4",
"hgvs_c": "c.795+1466G>A",
"hgvs_p": null,
"intron_rank": 10,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047282513.1",
"strand": false,
"transcript": "XM_047426557.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 311,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3583,
"cdna_start": null,
"cds_end": null,
"cds_length": 936,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 13,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047426558.1",
"gene_hgnc_id": 24849,
"gene_symbol": "GDPD4",
"hgvs_c": "c.795+1466G>A",
"hgvs_p": null,
"intron_rank": 10,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047282514.1",
"strand": false,
"transcript": "XM_047426558.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs779270640",
"effect": "missense_variant",
"frequency_reference_population": 0.000034087345,
"gene_hgnc_id": 24849,
"gene_symbol": "GDPD4",
"gnomad_exomes_ac": 53,
"gnomad_exomes_af": 0.0000362652,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131541,
"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": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.818,
"pos": 77243815,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.092,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_182833.3"
}
]
}