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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: 19-965043-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=965043&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 965043,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000263620.8",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARID3A",
"gene_hgnc_id": 3031,
"hgvs_c": "c.1161T>A",
"hgvs_p": "p.Asn387Lys",
"transcript": "NM_005224.3",
"protein_id": "NP_005215.1",
"transcript_support_level": null,
"aa_start": 387,
"aa_end": null,
"aa_length": 593,
"cds_start": 1161,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 1453,
"cdna_end": null,
"cdna_length": 5948,
"mane_select": "ENST00000263620.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARID3A",
"gene_hgnc_id": 3031,
"hgvs_c": "c.1161T>A",
"hgvs_p": "p.Asn387Lys",
"transcript": "ENST00000263620.8",
"protein_id": "ENSP00000263620.2",
"transcript_support_level": 1,
"aa_start": 387,
"aa_end": null,
"aa_length": 593,
"cds_start": 1161,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 1453,
"cdna_end": null,
"cdna_length": 5948,
"mane_select": "NM_005224.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "K",
"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": "ARID3A",
"gene_hgnc_id": 3031,
"hgvs_c": "c.702T>A",
"hgvs_p": "p.Asn234Lys",
"transcript": "ENST00000587532.5",
"protein_id": "ENSP00000464969.3",
"transcript_support_level": 5,
"aa_start": 234,
"aa_end": null,
"aa_length": 337,
"cds_start": 702,
"cds_end": null,
"cds_length": 1016,
"cdna_start": 702,
"cdna_end": null,
"cdna_length": 1016,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARID3A",
"gene_hgnc_id": 3031,
"hgvs_c": "c.1161T>A",
"hgvs_p": "p.Asn387Lys",
"transcript": "XM_005259513.6",
"protein_id": "XP_005259570.1",
"transcript_support_level": null,
"aa_start": 387,
"aa_end": null,
"aa_length": 593,
"cds_start": 1161,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 1560,
"cdna_end": null,
"cdna_length": 6055,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARID3A",
"gene_hgnc_id": 3031,
"hgvs_c": "c.1161T>A",
"hgvs_p": "p.Asn387Lys",
"transcript": "XM_005259514.5",
"protein_id": "XP_005259571.1",
"transcript_support_level": null,
"aa_start": 387,
"aa_end": null,
"aa_length": 593,
"cds_start": 1161,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 1591,
"cdna_end": null,
"cdna_length": 6086,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARID3A",
"gene_hgnc_id": 3031,
"hgvs_c": "c.1161T>A",
"hgvs_p": "p.Asn387Lys",
"transcript": "XM_017026445.2",
"protein_id": "XP_016881934.1",
"transcript_support_level": null,
"aa_start": 387,
"aa_end": null,
"aa_length": 593,
"cds_start": 1161,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 1617,
"cdna_end": null,
"cdna_length": 6112,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARID3A",
"gene_hgnc_id": 3031,
"hgvs_c": "c.1161T>A",
"hgvs_p": "p.Asn387Lys",
"transcript": "XM_047438380.1",
"protein_id": "XP_047294336.1",
"transcript_support_level": null,
"aa_start": 387,
"aa_end": null,
"aa_length": 494,
"cds_start": 1161,
"cds_end": null,
"cds_length": 1485,
"cdna_start": 1560,
"cdna_end": null,
"cdna_length": 5758,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "K",
"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": "ARID3A",
"gene_hgnc_id": 3031,
"hgvs_c": "c.486T>A",
"hgvs_p": "p.Asn162Lys",
"transcript": "XM_047438381.1",
"protein_id": "XP_047294337.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 368,
"cds_start": 486,
"cds_end": null,
"cds_length": 1107,
"cdna_start": 754,
"cdna_end": null,
"cdna_length": 5249,
"mane_select": null,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARID3A",
"gene_hgnc_id": 3031,
"hgvs_c": "n.354T>A",
"hgvs_p": null,
"transcript": "ENST00000585733.2",
"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": 581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ARID3A",
"gene_hgnc_id": 3031,
"dbsnp": "rs12608658",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.48157572746276855,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.195,
"revel_prediction": "Benign",
"alphamissense_score": 0.8007,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.53,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.16,
"phylop100way_prediction": "Benign",
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000263620.8",
"gene_symbol": "ARID3A",
"hgnc_id": 3031,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1161T>A",
"hgvs_p": "p.Asn387Lys"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}