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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: 20-10639874-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=10639874&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 10639874,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_000214.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAG1",
"gene_hgnc_id": 6188,
"hgvs_c": "c.3281G>A",
"hgvs_p": "p.Arg1094Gln",
"transcript": "NM_000214.3",
"protein_id": "NP_000205.1",
"transcript_support_level": null,
"aa_start": 1094,
"aa_end": null,
"aa_length": 1218,
"cds_start": 3281,
"cds_end": null,
"cds_length": 3657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000254958.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000214.3"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAG1",
"gene_hgnc_id": 6188,
"hgvs_c": "c.3281G>A",
"hgvs_p": "p.Arg1094Gln",
"transcript": "ENST00000254958.10",
"protein_id": "ENSP00000254958.4",
"transcript_support_level": 1,
"aa_start": 1094,
"aa_end": null,
"aa_length": 1218,
"cds_start": 3281,
"cds_end": null,
"cds_length": 3657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000214.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000254958.10"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAG1",
"gene_hgnc_id": 6188,
"hgvs_c": "c.3281G>A",
"hgvs_p": "p.Arg1094Gln",
"transcript": "ENST00000901230.1",
"protein_id": "ENSP00000571289.1",
"transcript_support_level": null,
"aa_start": 1094,
"aa_end": null,
"aa_length": 1218,
"cds_start": 3281,
"cds_end": null,
"cds_length": 3657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000901230.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAG1",
"gene_hgnc_id": 6188,
"hgvs_c": "c.3275G>A",
"hgvs_p": "p.Arg1092Gln",
"transcript": "ENST00000913738.1",
"protein_id": "ENSP00000583797.1",
"transcript_support_level": null,
"aa_start": 1092,
"aa_end": null,
"aa_length": 1216,
"cds_start": 3275,
"cds_end": null,
"cds_length": 3651,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913738.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAG1",
"gene_hgnc_id": 6188,
"hgvs_c": "c.3167G>A",
"hgvs_p": "p.Arg1056Gln",
"transcript": "ENST00000913736.1",
"protein_id": "ENSP00000583795.1",
"transcript_support_level": null,
"aa_start": 1056,
"aa_end": null,
"aa_length": 1180,
"cds_start": 3167,
"cds_end": null,
"cds_length": 3543,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913736.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAG1",
"gene_hgnc_id": 6188,
"hgvs_c": "c.3164G>A",
"hgvs_p": "p.Arg1055Gln",
"transcript": "ENST00000946613.1",
"protein_id": "ENSP00000616672.1",
"transcript_support_level": null,
"aa_start": 1055,
"aa_end": null,
"aa_length": 1179,
"cds_start": 3164,
"cds_end": null,
"cds_length": 3540,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946613.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAG1",
"gene_hgnc_id": 6188,
"hgvs_c": "c.3116G>A",
"hgvs_p": "p.Arg1039Gln",
"transcript": "ENST00000913737.1",
"protein_id": "ENSP00000583796.1",
"transcript_support_level": null,
"aa_start": 1039,
"aa_end": null,
"aa_length": 1163,
"cds_start": 3116,
"cds_end": null,
"cds_length": 3492,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913737.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAG1",
"gene_hgnc_id": 6188,
"hgvs_c": "n.3147G>A",
"hgvs_p": null,
"transcript": "ENST00000423891.6",
"protein_id": null,
"transcript_support_level": 2,
"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": "pseudogene",
"feature": "ENST00000423891.6"
},
{
"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": "JAG1",
"gene_hgnc_id": 6188,
"hgvs_c": "n.576G>A",
"hgvs_p": null,
"transcript": "ENST00000617357.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000617357.1"
}
],
"gene_symbol": "JAG1",
"gene_hgnc_id": 6188,
"dbsnp": "rs139629694",
"frequency_reference_population": 0.00020446046,
"hom_count_reference_population": 1,
"allele_count_reference_population": 330,
"gnomad_exomes_af": 0.000211376,
"gnomad_genomes_af": 0.000138016,
"gnomad_exomes_ac": 309,
"gnomad_genomes_ac": 21,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.27323633432388306,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.1899999976158142,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.395,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0959,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.17,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.66,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.19,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_000214.3",
"gene_symbol": "JAG1",
"hgnc_id": 6188,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3281G>A",
"hgvs_p": "p.Arg1094Gln"
}
],
"clinvar_disease": "Alagille syndrome due to a JAG1 point mutation,JAG1-related disorder,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "Alagille syndrome due to a JAG1 point mutation|not provided|JAG1-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}