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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: 19-40006099-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=40006099&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 40006099,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_178544.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF546",
"gene_hgnc_id": 28671,
"hgvs_c": "c.88C>T",
"hgvs_p": "p.Arg30Trp",
"transcript": "NM_178544.5",
"protein_id": "NP_848639.2",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 836,
"cds_start": 88,
"cds_end": null,
"cds_length": 2511,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000347077.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_178544.5"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF546",
"gene_hgnc_id": 28671,
"hgvs_c": "c.88C>T",
"hgvs_p": "p.Arg30Trp",
"transcript": "ENST00000347077.9",
"protein_id": "ENSP00000339823.3",
"transcript_support_level": 1,
"aa_start": 30,
"aa_end": null,
"aa_length": 836,
"cds_start": 88,
"cds_end": null,
"cds_length": 2511,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_178544.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000347077.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF546",
"gene_hgnc_id": 28671,
"hgvs_c": "c.-27C>T",
"hgvs_p": null,
"transcript": "ENST00000599504.5",
"protein_id": "ENSP00000469334.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 138,
"cds_start": null,
"cds_end": null,
"cds_length": 419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000599504.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF546",
"gene_hgnc_id": 28671,
"hgvs_c": "c.-27C>T",
"hgvs_p": null,
"transcript": "ENST00000601138.5",
"protein_id": "ENSP00000469168.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 125,
"cds_start": null,
"cds_end": null,
"cds_length": 378,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000601138.5"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF546",
"gene_hgnc_id": 28671,
"hgvs_c": "c.10C>T",
"hgvs_p": "p.Arg4Trp",
"transcript": "NM_001297763.2",
"protein_id": "NP_001284692.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 810,
"cds_start": 10,
"cds_end": null,
"cds_length": 2433,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001297763.2"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF546",
"gene_hgnc_id": 28671,
"hgvs_c": "c.10C>T",
"hgvs_p": "p.Arg4Trp",
"transcript": "ENST00000600094.5",
"protein_id": "ENSP00000469540.1",
"transcript_support_level": 2,
"aa_start": 4,
"aa_end": null,
"aa_length": 810,
"cds_start": 10,
"cds_end": null,
"cds_length": 2433,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000600094.5"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF546",
"gene_hgnc_id": 28671,
"hgvs_c": "c.10C>T",
"hgvs_p": "p.Arg4Trp",
"transcript": "ENST00000951738.1",
"protein_id": "ENSP00000621797.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 810,
"cds_start": 10,
"cds_end": null,
"cds_length": 2433,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951738.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF546",
"gene_hgnc_id": 28671,
"hgvs_c": "c.88C>T",
"hgvs_p": "p.Arg30Trp",
"transcript": "ENST00000595225.1",
"protein_id": "ENSP00000472403.1",
"transcript_support_level": 4,
"aa_start": 30,
"aa_end": null,
"aa_length": 123,
"cds_start": 88,
"cds_end": null,
"cds_length": 374,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000595225.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF546",
"gene_hgnc_id": 28671,
"hgvs_c": "c.-27C>T",
"hgvs_p": null,
"transcript": "ENST00000599504.5",
"protein_id": "ENSP00000469334.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 138,
"cds_start": null,
"cds_end": null,
"cds_length": 419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000599504.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF546",
"gene_hgnc_id": 28671,
"hgvs_c": "c.-27C>T",
"hgvs_p": null,
"transcript": "ENST00000601138.5",
"protein_id": "ENSP00000469168.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 125,
"cds_start": null,
"cds_end": null,
"cds_length": 378,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000601138.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ZNF546",
"gene_hgnc_id": 28671,
"hgvs_c": "c.76+6429C>T",
"hgvs_p": null,
"transcript": "ENST00000596894.5",
"protein_id": "ENSP00000470423.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 37,
"cds_start": null,
"cds_end": null,
"cds_length": 114,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000596894.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF546",
"gene_hgnc_id": 28671,
"hgvs_c": "n.*42C>T",
"hgvs_p": null,
"transcript": "ENST00000651981.1",
"protein_id": "ENSP00000499080.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000651981.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF546",
"gene_hgnc_id": 28671,
"hgvs_c": "n.*42C>T",
"hgvs_p": null,
"transcript": "ENST00000651981.1",
"protein_id": "ENSP00000499080.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000651981.1"
}
],
"gene_symbol": "ZNF546",
"gene_hgnc_id": 28671,
"dbsnp": "rs769296678",
"frequency_reference_population": 0.000011153107,
"hom_count_reference_population": 0,
"allele_count_reference_population": 18,
"gnomad_exomes_af": 0.0000102625,
"gnomad_genomes_af": 0.0000197013,
"gnomad_exomes_ac": 15,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.07855063676834106,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.045,
"revel_prediction": "Benign",
"alphamissense_score": 0.1457,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.67,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.177,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_178544.5",
"gene_symbol": "ZNF546",
"hgnc_id": 28671,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.88C>T",
"hgvs_p": "p.Arg30Trp"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}