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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: 2-26421396-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=26421396&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 5,
"criteria": [
"PVS1",
"PS3",
"PP5_Very_Strong",
"BS1_Supporting",
"BS2"
],
"effects": [
"stop_gained"
],
"gene_symbol": "DRC1",
"hgnc_id": 24245,
"hgvs_c": "c.352C>T",
"hgvs_p": "p.Gln118*",
"inheritance_mode": "AR,AD",
"pathogenic_score": 20,
"score": 15,
"transcript": "NM_145038.5",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PS3,PP5_Very_Strong,BS1_Supporting,BS2",
"acmg_score": 15,
"allele_count_reference_population": 962,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.62,
"chr": "2",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": "DRC1-related disorder,Primary ciliary dyskinesia,Primary ciliary dyskinesia 21,Spermatogenic failure 80,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:5 LP:2 US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.6200000047683716,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 740,
"aa_ref": "Q",
"aa_start": 118,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2487,
"cdna_start": 422,
"cds_end": null,
"cds_length": 2223,
"cds_start": 352,
"consequences": [
"stop_gained"
],
"exon_count": 17,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_145038.5",
"gene_hgnc_id": 24245,
"gene_symbol": "DRC1",
"hgvs_c": "c.352C>T",
"hgvs_p": "p.Gln118*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000288710.7",
"protein_coding": true,
"protein_id": "NP_659475.2",
"strand": true,
"transcript": "NM_145038.5",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 740,
"aa_ref": "Q",
"aa_start": 118,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2487,
"cdna_start": 422,
"cds_end": null,
"cds_length": 2223,
"cds_start": 352,
"consequences": [
"stop_gained"
],
"exon_count": 17,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000288710.7",
"gene_hgnc_id": 24245,
"gene_symbol": "DRC1",
"hgvs_c": "c.352C>T",
"hgvs_p": "p.Gln118*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_145038.5",
"protein_coding": true,
"protein_id": "ENSP00000288710.2",
"strand": true,
"transcript": "ENST00000288710.7",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1075,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000421869.5",
"gene_hgnc_id": 24245,
"gene_symbol": "DRC1",
"hgvs_c": "n.352C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000414375.1",
"strand": true,
"transcript": "ENST00000421869.5",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 715,
"aa_ref": "Q",
"aa_start": 118,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2403,
"cdna_start": 413,
"cds_end": null,
"cds_length": 2148,
"cds_start": 352,
"consequences": [
"stop_gained"
],
"exon_count": 17,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000868388.1",
"gene_hgnc_id": 24245,
"gene_symbol": "DRC1",
"hgvs_c": "c.352C>T",
"hgvs_p": "p.Gln118*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000538447.1",
"strand": true,
"transcript": "ENST00000868388.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 641,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2175,
"cdna_start": null,
"cds_end": null,
"cds_length": 1926,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000941553.1",
"gene_hgnc_id": 24245,
"gene_symbol": "DRC1",
"hgvs_c": "c.243+6965C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000611612.1",
"strand": true,
"transcript": "ENST00000941553.1",
"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": 579,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000487307.5",
"gene_hgnc_id": 24245,
"gene_symbol": "DRC1",
"hgvs_c": "n.243C>T",
"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": "ENST00000487307.5",
"transcript_support_level": 4
},
{
"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": 581,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000497651.1",
"gene_hgnc_id": 24245,
"gene_symbol": "DRC1",
"hgvs_c": "n.242C>T",
"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": "ENST00000497651.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2229,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 16,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000649059.1",
"gene_hgnc_id": 24245,
"gene_symbol": "DRC1",
"hgvs_c": "n.337C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000497543.1",
"strand": true,
"transcript": "ENST00000649059.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs142371860",
"effect": "stop_gained",
"frequency_reference_population": 0.0005966454,
"gene_hgnc_id": 24245,
"gene_symbol": "DRC1",
"gnomad_exomes_ac": 919,
"gnomad_exomes_af": 0.000629331,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_ac": 43,
"gnomad_genomes_af": 0.000282768,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 2,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"phenotype_combined": "Primary ciliary dyskinesia 21|Primary ciliary dyskinesia|not provided|not specified|Primary ciliary dyskinesia;Primary ciliary dyskinesia 21|DRC1-related disorder|Spermatogenic failure 80",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.875,
"pos": 26421396,
"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_145038.5"
}
]
}