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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: 21-34370518-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=34370518&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "21",
"pos": 34370518,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000290310.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNE2",
"gene_hgnc_id": 6242,
"hgvs_c": "c.40G>A",
"hgvs_p": "p.Val14Ile",
"transcript": "NM_172201.2",
"protein_id": "NP_751951.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 123,
"cds_start": 40,
"cds_end": null,
"cds_length": 372,
"cdna_start": 198,
"cdna_end": null,
"cdna_length": 1061,
"mane_select": "ENST00000290310.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNE2",
"gene_hgnc_id": 6242,
"hgvs_c": "c.40G>A",
"hgvs_p": "p.Val14Ile",
"transcript": "ENST00000290310.4",
"protein_id": "ENSP00000290310.2",
"transcript_support_level": 1,
"aa_start": 14,
"aa_end": null,
"aa_length": 123,
"cds_start": 40,
"cds_end": null,
"cds_length": 372,
"cdna_start": 198,
"cdna_end": null,
"cdna_length": 1061,
"mane_select": "NM_172201.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNE2",
"gene_hgnc_id": 6242,
"hgvs_c": "c.40G>A",
"hgvs_p": "p.Val14Ile",
"transcript": "ENST00000715813.1",
"protein_id": "ENSP00000520524.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 123,
"cds_start": 40,
"cds_end": null,
"cds_length": 372,
"cdna_start": 2755,
"cdna_end": null,
"cdna_length": 3243,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000225555",
"gene_hgnc_id": null,
"hgvs_c": "n.771C>T",
"hgvs_p": null,
"transcript": "ENST00000440403.2",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2643,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000225555",
"gene_hgnc_id": null,
"hgvs_c": "n.1216C>T",
"hgvs_p": null,
"transcript": "ENST00000813044.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1641,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000225555",
"gene_hgnc_id": null,
"hgvs_c": "n.792C>T",
"hgvs_p": null,
"transcript": "ENST00000813045.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 796,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC105372791",
"gene_hgnc_id": null,
"hgvs_c": "n.769C>T",
"hgvs_p": null,
"transcript": "NR_188571.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2734,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC105372791",
"gene_hgnc_id": null,
"hgvs_c": "n.769C>T",
"hgvs_p": null,
"transcript": "NR_188572.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1116,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000225555",
"gene_hgnc_id": null,
"hgvs_c": "n.*1C>T",
"hgvs_p": null,
"transcript": "ENST00000813046.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 701,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "KCNE2",
"gene_hgnc_id": 6242,
"dbsnp": "rs142153692",
"frequency_reference_population": 0.00019266916,
"hom_count_reference_population": 2,
"allele_count_reference_population": 311,
"gnomad_exomes_af": 0.000158015,
"gnomad_genomes_af": 0.000525341,
"gnomad_exomes_ac": 231,
"gnomad_genomes_ac": 80,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.009433716535568237,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.233,
"revel_prediction": "Benign",
"alphamissense_score": 0.0787,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.37,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.771,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000290310.4",
"gene_symbol": "KCNE2",
"hgnc_id": 6242,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.40G>A",
"hgvs_p": "p.Val14Ile"
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong"
],
"verdict": "Benign",
"transcript": "ENST00000440403.2",
"gene_symbol": "ENSG00000225555",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.771C>T",
"hgvs_p": null
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong"
],
"verdict": "Benign",
"transcript": "NR_188571.1",
"gene_symbol": "LOC105372791",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.769C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Cardiovascular phenotype,Long QT syndrome,Long QT syndrome 6,not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4 O:1",
"phenotype_combined": "not provided|Long QT syndrome|Cardiovascular phenotype|Long QT syndrome 6",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}