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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: 20-10644907-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=10644907&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 10644907,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000254958.10",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAG1",
"gene_hgnc_id": 6188,
"hgvs_c": "c.2300C>T",
"hgvs_p": "p.Thr767Met",
"transcript": "NM_000214.3",
"protein_id": "NP_000205.1",
"transcript_support_level": null,
"aa_start": 767,
"aa_end": null,
"aa_length": 1218,
"cds_start": 2300,
"cds_end": null,
"cds_length": 3657,
"cdna_start": 2769,
"cdna_end": null,
"cdna_length": 5940,
"mane_select": "ENST00000254958.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAG1",
"gene_hgnc_id": 6188,
"hgvs_c": "c.2300C>T",
"hgvs_p": "p.Thr767Met",
"transcript": "ENST00000254958.10",
"protein_id": "ENSP00000254958.4",
"transcript_support_level": 1,
"aa_start": 767,
"aa_end": null,
"aa_length": 1218,
"cds_start": 2300,
"cds_end": null,
"cds_length": 3657,
"cdna_start": 2769,
"cdna_end": null,
"cdna_length": 5940,
"mane_select": "NM_000214.3",
"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": 16,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAG1",
"gene_hgnc_id": 6188,
"hgvs_c": "n.2166C>T",
"hgvs_p": null,
"transcript": "ENST00000423891.6",
"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": 3758,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAG1",
"gene_hgnc_id": 6188,
"hgvs_c": "n.697C>T",
"hgvs_p": null,
"transcript": "ENST00000488480.2",
"protein_id": null,
"transcript_support_level": 4,
"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": 1161,
"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": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAG1",
"gene_hgnc_id": 6188,
"hgvs_c": "n.2889C>T",
"hgvs_p": null,
"transcript": "ENST00000617965.2",
"protein_id": null,
"transcript_support_level": 5,
"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": 3385,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "JAG1",
"gene_hgnc_id": 6188,
"dbsnp": "rs140330283",
"frequency_reference_population": 0.00012267978,
"hom_count_reference_population": 0,
"allele_count_reference_population": 198,
"gnomad_exomes_af": 0.000128605,
"gnomad_genomes_af": 0.0000657384,
"gnomad_exomes_ac": 188,
"gnomad_genomes_ac": 10,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7947710752487183,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.12999999523162842,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.632,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.119,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.05,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.627,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.13,
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "PP3,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 9,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000254958.10",
"gene_symbol": "JAG1",
"hgnc_id": 6188,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2300C>T",
"hgvs_p": "p.Thr767Met"
}
],
"clinvar_disease": " Type 2HH, and posterior embryotoxon, axonal, congenital heart defects,Alagille syndrome due to a JAG1 point mutation,Cardiovascular phenotype,Charcot-Marie-Tooth disease,Deafness,Isolated Nonsyndromic Congenital Heart Disease,Tetralogy of Fallot,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:2",
"phenotype_combined": "Isolated Nonsyndromic Congenital Heart Disease|Cardiovascular phenotype|not provided|Deafness, congenital heart defects, and posterior embryotoxon;Alagille syndrome due to a JAG1 point mutation;Tetralogy of Fallot;Charcot-Marie-Tooth disease, axonal, Type 2HH|Alagille syndrome due to a JAG1 point mutation",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}