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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: 1-26913409-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=26913409&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PP3_Strong",
"BP6_Moderate"
],
"effects": [
"missense_variant",
"splice_region_variant"
],
"gene_symbol": "NR0B2",
"hgnc_id": 7961,
"hgvs_c": "c.532G>A",
"hgvs_p": "p.Asp178Asn",
"inheritance_mode": "Unknown",
"pathogenic_score": 4,
"score": 2,
"transcript": "NM_021969.3",
"verdict": "Uncertain_significance"
},
{
"benign_score": 6,
"criteria": [
"PP3_Strong",
"BP6_Moderate",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "NUDC",
"hgnc_id": 8045,
"hgvs_c": "c.93+2174C>T",
"hgvs_p": null,
"inheritance_mode": "AD",
"pathogenic_score": 4,
"score": -2,
"transcript": "ENST00000435827.6",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Strong,BP6_Moderate",
"acmg_score": 2,
"allele_count_reference_population": 146,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.2001,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.17,
"chr": "1",
"clinvar_classification": "Likely benign",
"clinvar_disease": "NR0B2-related disorder,not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.6348392367362976,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 257,
"aa_ref": "D",
"aa_start": 178,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1165,
"cdna_start": 567,
"cds_end": null,
"cds_length": 774,
"cds_start": 532,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_021969.3",
"gene_hgnc_id": 7961,
"gene_symbol": "NR0B2",
"hgvs_c": "c.532G>A",
"hgvs_p": "p.Asp178Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000254227.4",
"protein_coding": true,
"protein_id": "NP_068804.1",
"strand": false,
"transcript": "NM_021969.3",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 257,
"aa_ref": "D",
"aa_start": 178,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1165,
"cdna_start": 567,
"cds_end": null,
"cds_length": 774,
"cds_start": 532,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000254227.4",
"gene_hgnc_id": 7961,
"gene_symbol": "NR0B2",
"hgvs_c": "c.532G>A",
"hgvs_p": "p.Asp178Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_021969.3",
"protein_coding": true,
"protein_id": "ENSP00000254227.3",
"strand": false,
"transcript": "ENST00000254227.4",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 207,
"aa_ref": "D",
"aa_start": 178,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1483,
"cdna_start": 567,
"cds_end": null,
"cds_length": 624,
"cds_start": 532,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_011542297.4",
"gene_hgnc_id": 7961,
"gene_symbol": "NR0B2",
"hgvs_c": "c.532G>A",
"hgvs_p": "p.Asp178Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011540599.1",
"strand": false,
"transcript": "XM_011542297.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 185,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 821,
"cdna_start": null,
"cds_end": null,
"cds_length": 558,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000435827.6",
"gene_hgnc_id": 8045,
"gene_symbol": "NUDC",
"hgvs_c": "c.93+2174C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000404020.2",
"strand": true,
"transcript": "ENST00000435827.6",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 335,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2009,
"cdna_start": null,
"cds_end": null,
"cds_length": 1008,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_024452486.2",
"gene_hgnc_id": 8045,
"gene_symbol": "NUDC",
"hgvs_c": "c.93+2174C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024308254.1",
"strand": true,
"transcript": "XM_024452486.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 335,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2718,
"cdna_start": null,
"cds_end": null,
"cds_length": 1008,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047439143.1",
"gene_hgnc_id": 8045,
"gene_symbol": "NUDC",
"hgvs_c": "c.93+2174C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047295099.1",
"strand": true,
"transcript": "XM_047439143.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 335,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1882,
"cdna_start": null,
"cds_end": null,
"cds_length": 1008,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 10,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047439200.1",
"gene_hgnc_id": 8045,
"gene_symbol": "NUDC",
"hgvs_c": "c.93+2174C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047295156.1",
"strand": true,
"transcript": "XM_047439200.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 335,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2606,
"cdna_start": null,
"cds_end": null,
"cds_length": 1008,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 10,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047439206.1",
"gene_hgnc_id": 8045,
"gene_symbol": "NUDC",
"hgvs_c": "c.93+2174C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047295162.1",
"strand": true,
"transcript": "XM_047439206.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999991658220094,
"dbsnp": "rs201991593",
"effect": "missense_variant,splice_region_variant",
"frequency_reference_population": 0.00009045658,
"gene_hgnc_id": 7961,
"gene_symbol": "NR0B2",
"gnomad_exomes_ac": 136,
"gnomad_exomes_af": 0.0000930342,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 10,
"gnomad_genomes_af": 0.0000657004,
"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": "Likely benign",
"phenotype_combined": "not specified|NR0B2-related disorder",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.568,
"pos": 26913409,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.74,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 1,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_021969.3"
}
]
}