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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: 20-2558734-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=2558734&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "TMC2",
"hgnc_id": 16527,
"hgvs_c": "c.361C>G",
"hgvs_p": "p.Pro121Ala",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_080751.3",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000298229",
"hgnc_id": null,
"hgvs_c": "n.60+406G>C",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -2,
"transcript": "ENST00000753996.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 21,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0662,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.68,
"chr": "20",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.04922017455101013,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 906,
"aa_ref": "P",
"aa_start": 121,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4999,
"cdna_start": 410,
"cds_end": null,
"cds_length": 2721,
"cds_start": 361,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_080751.3",
"gene_hgnc_id": 16527,
"gene_symbol": "TMC2",
"hgvs_c": "c.361C>G",
"hgvs_p": "p.Pro121Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000358864.2",
"protein_coding": true,
"protein_id": "NP_542789.2",
"strand": true,
"transcript": "NM_080751.3",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 906,
"aa_ref": "P",
"aa_start": 121,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4999,
"cdna_start": 410,
"cds_end": null,
"cds_length": 2721,
"cds_start": 361,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000358864.2",
"gene_hgnc_id": 16527,
"gene_symbol": "TMC2",
"hgvs_c": "c.361C>G",
"hgvs_p": "p.Pro121Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_080751.3",
"protein_coding": true,
"protein_id": "ENSP00000351732.1",
"strand": true,
"transcript": "ENST00000358864.2",
"transcript_support_level": 1
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 931,
"aa_ref": "P",
"aa_start": 146,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3209,
"cdna_start": 570,
"cds_end": null,
"cds_length": 2796,
"cds_start": 436,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_005260660.5",
"gene_hgnc_id": 16527,
"gene_symbol": "TMC2",
"hgvs_c": "c.436C>G",
"hgvs_p": "p.Pro146Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005260717.1",
"strand": true,
"transcript": "XM_005260660.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3477,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 15,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000644205.1",
"gene_hgnc_id": 16527,
"gene_symbol": "TMC2",
"hgvs_c": "n.520C>G",
"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": "ENST00000644205.1",
"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": 2848,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XR_001754152.2",
"gene_hgnc_id": 16527,
"gene_symbol": "TMC2",
"hgvs_c": "n.570C>G",
"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": "XR_001754152.2",
"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": 664,
"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": "ENST00000753996.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000298229",
"hgvs_c": "n.60+406G>C",
"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": "ENST00000753996.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs372993579",
"effect": "missense_variant",
"frequency_reference_population": 0.000014681639,
"gene_hgnc_id": 16527,
"gene_symbol": "TMC2",
"gnomad_exomes_ac": 21,
"gnomad_exomes_af": 0.0000146816,
"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": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.756,
"pos": 2558734,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.044,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_080751.3"
}
]
}