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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: 7-21901190-TGAAGAGC-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=21901190&ref=TGAAGAGC&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 21901190,
"ref": "TGAAGAGC",
"alt": "T",
"effect": "frameshift_variant",
"transcript": "ENST00000409508.8",
"consequences": [
{
"aa_ref": "SEE",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 82,
"exon_rank_end": null,
"exon_count": 82,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH11",
"gene_hgnc_id": 2942,
"hgvs_c": "c.13494_13500delCGAAGAG",
"hgvs_p": "p.Ser4498fs",
"transcript": "NM_001277115.2",
"protein_id": "NP_001264044.1",
"transcript_support_level": null,
"aa_start": 4498,
"aa_end": null,
"aa_length": 4516,
"cds_start": 13494,
"cds_end": null,
"cds_length": 13551,
"cdna_start": 13701,
"cdna_end": null,
"cdna_length": 14343,
"mane_select": "ENST00000409508.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SEE",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 82,
"exon_rank_end": null,
"exon_count": 82,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH11",
"gene_hgnc_id": 2942,
"hgvs_c": "c.13494_13500delCGAAGAG",
"hgvs_p": "p.Ser4498fs",
"transcript": "ENST00000409508.8",
"protein_id": "ENSP00000475939.1",
"transcript_support_level": 5,
"aa_start": 4498,
"aa_end": null,
"aa_length": 4516,
"cds_start": 13494,
"cds_end": null,
"cds_length": 13551,
"cdna_start": 13701,
"cdna_end": null,
"cdna_length": 14343,
"mane_select": "NM_001277115.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDCA7L",
"gene_hgnc_id": 30777,
"hgvs_c": "c.*1125_*1131delGCTCTTC",
"hgvs_p": null,
"transcript": "NM_018719.5",
"protein_id": "NP_061189.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 454,
"cds_start": -4,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2883,
"mane_select": "ENST00000406877.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDCA7L",
"gene_hgnc_id": 30777,
"hgvs_c": "c.*1125_*1131delGCTCTTC",
"hgvs_p": null,
"transcript": "ENST00000406877.8",
"protein_id": "ENSP00000383986.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 454,
"cds_start": -4,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2883,
"mane_select": "NM_018719.5",
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDCA7L",
"gene_hgnc_id": 30777,
"hgvs_c": "n.1647_1653delGCTCTTC",
"hgvs_p": null,
"transcript": "ENST00000488845.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 1943,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDCA7L",
"gene_hgnc_id": 30777,
"hgvs_c": "c.*1125_*1131delGCTCTTC",
"hgvs_p": null,
"transcript": "NM_001127370.3",
"protein_id": "NP_001120842.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 420,
"cds_start": -4,
"cds_end": null,
"cds_length": 1263,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2937,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDCA7L",
"gene_hgnc_id": 30777,
"hgvs_c": "c.*1125_*1131delGCTCTTC",
"hgvs_p": null,
"transcript": "ENST00000356195.9",
"protein_id": "ENSP00000348523.5",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 420,
"cds_start": -4,
"cds_end": null,
"cds_length": 1263,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2915,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CDCA7L",
"gene_hgnc_id": 30777,
"hgvs_c": "c.*1125_*1131delGCTCTTC",
"hgvs_p": null,
"transcript": "NM_001127371.3",
"protein_id": "NP_001120843.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 408,
"cds_start": -4,
"cds_end": null,
"cds_length": 1227,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2745,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH11",
"gene_hgnc_id": 2942,
"hgvs_c": "n.*75_*81delGAAGAGC",
"hgvs_p": null,
"transcript": "ENST00000479878.1",
"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": 784,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DNAH11",
"gene_hgnc_id": 2942,
"dbsnp": "rs1212535211",
"frequency_reference_population": 0.00000410513,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000410513,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 8.935,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Strong,PP5_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PVS1_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000409508.8",
"gene_symbol": "DNAH11",
"hgnc_id": 2942,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.13494_13500delCGAAGAG",
"hgvs_p": "p.Ser4498fs"
},
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3",
"PP5_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000406877.8",
"gene_symbol": "CDCA7L",
"hgnc_id": 30777,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*1125_*1131delGCTCTTC",
"hgvs_p": null
}
],
"clinvar_disease": "Primary ciliary dyskinesia",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Primary ciliary dyskinesia",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}