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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: 11-36575309-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=36575309&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 36575309,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000299440.6",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"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": "RAG1",
"gene_hgnc_id": 9831,
"hgvs_c": "c.2005G>A",
"hgvs_p": "p.Glu669Lys",
"transcript": "NM_000448.3",
"protein_id": "NP_000439.2",
"transcript_support_level": null,
"aa_start": 669,
"aa_end": null,
"aa_length": 1043,
"cds_start": 2005,
"cds_end": null,
"cds_length": 3132,
"cdna_start": 2135,
"cdna_end": null,
"cdna_length": 6588,
"mane_select": "ENST00000299440.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"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": "RAG1",
"gene_hgnc_id": 9831,
"hgvs_c": "c.2005G>A",
"hgvs_p": "p.Glu669Lys",
"transcript": "ENST00000299440.6",
"protein_id": "ENSP00000299440.5",
"transcript_support_level": 1,
"aa_start": 669,
"aa_end": null,
"aa_length": 1043,
"cds_start": 2005,
"cds_end": null,
"cds_length": 3132,
"cdna_start": 2135,
"cdna_end": null,
"cdna_length": 6588,
"mane_select": "NM_000448.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAG1",
"gene_hgnc_id": 9831,
"hgvs_c": "n.2005G>A",
"hgvs_p": null,
"transcript": "ENST00000534663.1",
"protein_id": "ENSP00000434610.1",
"transcript_support_level": 1,
"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": 3707,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAG1",
"gene_hgnc_id": 9831,
"hgvs_c": "c.2005G>A",
"hgvs_p": "p.Glu669Lys",
"transcript": "NM_001377277.1",
"protein_id": "NP_001364206.1",
"transcript_support_level": null,
"aa_start": 669,
"aa_end": null,
"aa_length": 1043,
"cds_start": 2005,
"cds_end": null,
"cds_length": 3132,
"cdna_start": 2478,
"cdna_end": null,
"cdna_length": 6931,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAG1",
"gene_hgnc_id": 9831,
"hgvs_c": "c.2005G>A",
"hgvs_p": "p.Glu669Lys",
"transcript": "NM_001377278.1",
"protein_id": "NP_001364207.1",
"transcript_support_level": null,
"aa_start": 669,
"aa_end": null,
"aa_length": 1043,
"cds_start": 2005,
"cds_end": null,
"cds_length": 3132,
"cdna_start": 2416,
"cdna_end": null,
"cdna_length": 6869,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAG1",
"gene_hgnc_id": 9831,
"hgvs_c": "c.2005G>A",
"hgvs_p": "p.Glu669Lys",
"transcript": "NM_001377279.1",
"protein_id": "NP_001364208.1",
"transcript_support_level": null,
"aa_start": 669,
"aa_end": null,
"aa_length": 1043,
"cds_start": 2005,
"cds_end": null,
"cds_length": 3132,
"cdna_start": 2318,
"cdna_end": null,
"cdna_length": 6771,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"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": "RAG1",
"gene_hgnc_id": 9831,
"hgvs_c": "c.2005G>A",
"hgvs_p": "p.Glu669Lys",
"transcript": "NM_001377280.1",
"protein_id": "NP_001364209.1",
"transcript_support_level": null,
"aa_start": 669,
"aa_end": null,
"aa_length": 1043,
"cds_start": 2005,
"cds_end": null,
"cds_length": 3132,
"cdna_start": 2204,
"cdna_end": null,
"cdna_length": 6657,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAG1",
"gene_hgnc_id": 9831,
"hgvs_c": "c.2005G>A",
"hgvs_p": "p.Glu669Lys",
"transcript": "NM_001440488.1",
"protein_id": "NP_001427417.1",
"transcript_support_level": null,
"aa_start": 669,
"aa_end": null,
"aa_length": 1043,
"cds_start": 2005,
"cds_end": null,
"cds_length": 3132,
"cdna_start": 2302,
"cdna_end": null,
"cdna_length": 6755,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"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": "RAG1",
"gene_hgnc_id": 9831,
"hgvs_c": "c.2005G>A",
"hgvs_p": "p.Glu669Lys",
"transcript": "NM_001440489.1",
"protein_id": "NP_001427418.1",
"transcript_support_level": null,
"aa_start": 669,
"aa_end": null,
"aa_length": 1043,
"cds_start": 2005,
"cds_end": null,
"cds_length": 3132,
"cdna_start": 2705,
"cdna_end": null,
"cdna_length": 7158,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAG1",
"gene_hgnc_id": 9831,
"hgvs_c": "c.2005G>A",
"hgvs_p": "p.Glu669Lys",
"transcript": "ENST00000697713.1",
"protein_id": "ENSP00000513411.1",
"transcript_support_level": null,
"aa_start": 669,
"aa_end": null,
"aa_length": 1043,
"cds_start": 2005,
"cds_end": null,
"cds_length": 3132,
"cdna_start": 2301,
"cdna_end": null,
"cdna_length": 6754,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"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": "RAG1",
"gene_hgnc_id": 9831,
"hgvs_c": "c.2005G>A",
"hgvs_p": "p.Glu669Lys",
"transcript": "ENST00000697714.1",
"protein_id": "ENSP00000513412.1",
"transcript_support_level": null,
"aa_start": 669,
"aa_end": null,
"aa_length": 1043,
"cds_start": 2005,
"cds_end": null,
"cds_length": 3132,
"cdna_start": 2185,
"cdna_end": null,
"cdna_length": 6638,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAG1",
"gene_hgnc_id": 9831,
"hgvs_c": "c.2005G>A",
"hgvs_p": "p.Glu669Lys",
"transcript": "ENST00000697715.1",
"protein_id": "ENSP00000513413.1",
"transcript_support_level": null,
"aa_start": 669,
"aa_end": null,
"aa_length": 1043,
"cds_start": 2005,
"cds_end": null,
"cds_length": 3132,
"cdna_start": 2428,
"cdna_end": null,
"cdna_length": 6881,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAG1",
"gene_hgnc_id": 9831,
"hgvs_c": "c.2005G>A",
"hgvs_p": "p.Glu669Lys",
"transcript": "XM_047427384.1",
"protein_id": "XP_047283340.1",
"transcript_support_level": null,
"aa_start": 669,
"aa_end": null,
"aa_length": 1043,
"cds_start": 2005,
"cds_end": null,
"cds_length": 3132,
"cdna_start": 3306,
"cdna_end": null,
"cdna_length": 7759,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RAG1",
"gene_hgnc_id": 9831,
"dbsnp": "rs878853004",
"frequency_reference_population": 0.0000034203142,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000342031,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9116148948669434,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.836,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.7114,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.42,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.602,
"phylop100way_prediction": "Pathogenic",
"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": 15,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PM5,PP2,PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 15,
"benign_score": 0,
"pathogenic_score": 15,
"criteria": [
"PM2",
"PM5",
"PP2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000299440.6",
"gene_symbol": "RAG1",
"hgnc_id": 9831,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2005G>A",
"hgvs_p": "p.Glu669Lys"
}
],
"clinvar_disease": " B cell-negative, NK cell-positive, T cell-negative, autosomal recessive,Combined immunodeficiency due to partial RAG1 deficiency,Combined immunodeficiency with skin granulomas,Histiocytic medullary reticulosis,Severe combined immunodeficiency,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:2",
"phenotype_combined": "not provided|Combined immunodeficiency with skin granulomas;Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive|Combined immunodeficiency due to partial RAG1 deficiency;Histiocytic medullary reticulosis;Combined immunodeficiency with skin granulomas;Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}