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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: 13-95760073-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=95760073&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"effects": [
"stop_gained"
],
"gene_symbol": "DNAJC3",
"hgnc_id": 9439,
"hgvs_c": "c.580C>T",
"hgvs_p": "p.Arg194*",
"inheritance_mode": "AR,AD",
"pathogenic_score": 11,
"score": 11,
"transcript": "NM_006260.5",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_score": 11,
"allele_count_reference_population": 5,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.62,
"chr": "13",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Juvenile-onset diabetes mellitus-central and peripheral neurodegeneration syndrome,Prostate cancer",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.6200000047683716,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 504,
"aa_ref": "R",
"aa_start": 194,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5590,
"cdna_start": 697,
"cds_end": null,
"cds_length": 1515,
"cds_start": 580,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_006260.5",
"gene_hgnc_id": 9439,
"gene_symbol": "DNAJC3",
"hgvs_c": "c.580C>T",
"hgvs_p": "p.Arg194*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000602402.6",
"protein_coding": true,
"protein_id": "NP_006251.1",
"strand": true,
"transcript": "NM_006260.5",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 504,
"aa_ref": "R",
"aa_start": 194,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5590,
"cdna_start": 697,
"cds_end": null,
"cds_length": 1515,
"cds_start": 580,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000602402.6",
"gene_hgnc_id": 9439,
"gene_symbol": "DNAJC3",
"hgvs_c": "c.580C>T",
"hgvs_p": "p.Arg194*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006260.5",
"protein_coding": true,
"protein_id": "ENSP00000473631.1",
"strand": true,
"transcript": "ENST00000602402.6",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 550,
"aa_ref": "R",
"aa_start": 194,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5727,
"cdna_start": 697,
"cds_end": null,
"cds_length": 1653,
"cds_start": 580,
"consequences": [
"stop_gained"
],
"exon_count": 13,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000947240.1",
"gene_hgnc_id": 9439,
"gene_symbol": "DNAJC3",
"hgvs_c": "c.580C>T",
"hgvs_p": "p.Arg194*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000617299.1",
"strand": true,
"transcript": "ENST00000947240.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 533,
"aa_ref": "R",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3639,
"cdna_start": 807,
"cds_end": null,
"cds_length": 1602,
"cds_start": 667,
"consequences": [
"stop_gained"
],
"exon_count": 13,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000880232.1",
"gene_hgnc_id": 9439,
"gene_symbol": "DNAJC3",
"hgvs_c": "c.667C>T",
"hgvs_p": "p.Arg223*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000550291.1",
"strand": true,
"transcript": "ENST00000880232.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 506,
"aa_ref": "R",
"aa_start": 194,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3117,
"cdna_start": 681,
"cds_end": null,
"cds_length": 1521,
"cds_start": 580,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000947242.1",
"gene_hgnc_id": 9439,
"gene_symbol": "DNAJC3",
"hgvs_c": "c.580C>T",
"hgvs_p": "p.Arg194*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000617301.1",
"strand": true,
"transcript": "ENST00000947242.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 503,
"aa_ref": "R",
"aa_start": 193,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1723,
"cdna_start": 719,
"cds_end": null,
"cds_length": 1512,
"cds_start": 577,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000947243.1",
"gene_hgnc_id": 9439,
"gene_symbol": "DNAJC3",
"hgvs_c": "c.577C>T",
"hgvs_p": "p.Arg193*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000617302.1",
"strand": true,
"transcript": "ENST00000947243.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 486,
"aa_ref": "R",
"aa_start": 176,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1646,
"cdna_start": 629,
"cds_end": null,
"cds_length": 1461,
"cds_start": 526,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000935418.1",
"gene_hgnc_id": 9439,
"gene_symbol": "DNAJC3",
"hgvs_c": "c.526C>T",
"hgvs_p": "p.Arg176*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000605477.1",
"strand": true,
"transcript": "ENST00000935418.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 467,
"aa_ref": "R",
"aa_start": 157,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1622,
"cdna_start": 593,
"cds_end": null,
"cds_length": 1404,
"cds_start": 469,
"consequences": [
"stop_gained"
],
"exon_count": 11,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000880233.1",
"gene_hgnc_id": 9439,
"gene_symbol": "DNAJC3",
"hgvs_c": "c.469C>T",
"hgvs_p": "p.Arg157*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000550292.1",
"strand": true,
"transcript": "ENST00000880233.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 464,
"aa_ref": "R",
"aa_start": 194,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5456,
"cdna_start": 704,
"cds_end": null,
"cds_length": 1395,
"cds_start": 580,
"consequences": [
"stop_gained"
],
"exon_count": 11,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000947241.1",
"gene_hgnc_id": 9439,
"gene_symbol": "DNAJC3",
"hgvs_c": "c.580C>T",
"hgvs_p": "p.Arg194*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000617300.1",
"strand": true,
"transcript": "ENST00000947241.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 453,
"aa_ref": "R",
"aa_start": 143,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2273,
"cdna_start": 525,
"cds_end": null,
"cds_length": 1362,
"cds_start": 427,
"consequences": [
"stop_gained"
],
"exon_count": 11,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000376795.6",
"gene_hgnc_id": 9439,
"gene_symbol": "DNAJC3",
"hgvs_c": "c.427C>T",
"hgvs_p": "p.Arg143*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000365991.6",
"strand": true,
"transcript": "ENST00000376795.6",
"transcript_support_level": 5
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 533,
"aa_ref": "R",
"aa_start": 223,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5677,
"cdna_start": 784,
"cds_end": null,
"cds_length": 1602,
"cds_start": 667,
"consequences": [
"stop_gained"
],
"exon_count": 13,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_011521104.3",
"gene_hgnc_id": 9439,
"gene_symbol": "DNAJC3",
"hgvs_c": "c.667C>T",
"hgvs_p": "p.Arg223*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011519406.1",
"strand": true,
"transcript": "XM_011521104.3",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs727502865",
"effect": "stop_gained",
"frequency_reference_population": 0.0000031126544,
"gene_hgnc_id": 9439,
"gene_symbol": "DNAJC3",
"gnomad_exomes_ac": 3,
"gnomad_exomes_af": 0.0000020629,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131505,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Juvenile-onset diabetes mellitus-central and peripheral neurodegeneration syndrome|Prostate cancer",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.39,
"pos": 95760073,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_006260.5"
}
]
}