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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: 1-97098598-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=97098598&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "DPYD",
"hgnc_id": 3012,
"hgvs_c": "c.2657G>C",
"hgvs_p": "p.Arg886Pro",
"inheritance_mode": "AR",
"pathogenic_score": 4,
"score": 4,
"transcript": "NM_000110.4",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "DPYD-AS1",
"hgnc_id": 40195,
"hgvs_c": "n.64+2612C>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 4,
"score": 4,
"transcript": "ENST00000422980.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_score": 4,
"allele_count_reference_population": 0,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.953,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.18,
"chr": "1",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8629887104034424,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1025,
"aa_ref": "R",
"aa_start": 886,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4423,
"cdna_start": 2769,
"cds_end": null,
"cds_length": 3078,
"cds_start": 2657,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "NM_000110.4",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2657G>C",
"hgvs_p": "p.Arg886Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000370192.8",
"protein_coding": true,
"protein_id": "NP_000101.2",
"strand": false,
"transcript": "NM_000110.4",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1025,
"aa_ref": "R",
"aa_start": 886,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4423,
"cdna_start": 2769,
"cds_end": null,
"cds_length": 3078,
"cds_start": 2657,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000370192.8",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2657G>C",
"hgvs_p": "p.Arg886Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000110.4",
"protein_coding": true,
"protein_id": "ENSP00000359211.3",
"strand": false,
"transcript": "ENST00000370192.8",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1081,
"aa_ref": "R",
"aa_start": 942,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4583,
"cdna_start": 2932,
"cds_end": null,
"cds_length": 3246,
"cds_start": 2825,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000876340.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2825G>C",
"hgvs_p": "p.Arg942Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546399.1",
"strand": false,
"transcript": "ENST00000876340.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1060,
"aa_ref": "R",
"aa_start": 921,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4525,
"cdna_start": 2874,
"cds_end": null,
"cds_length": 3183,
"cds_start": 2762,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000969915.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2762G>C",
"hgvs_p": "p.Arg921Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000639974.1",
"strand": false,
"transcript": "ENST00000969915.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1058,
"aa_ref": "R",
"aa_start": 919,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4528,
"cdna_start": 2874,
"cds_end": null,
"cds_length": 3177,
"cds_start": 2756,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000876335.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2756G>C",
"hgvs_p": "p.Arg919Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546394.1",
"strand": false,
"transcript": "ENST00000876335.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1055,
"aa_ref": "R",
"aa_start": 886,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4527,
"cdna_start": 2787,
"cds_end": null,
"cds_length": 3168,
"cds_start": 2657,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000969914.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2657G>C",
"hgvs_p": "p.Arg886Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000639973.1",
"strand": false,
"transcript": "ENST00000969914.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1002,
"aa_ref": "R",
"aa_start": 863,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4374,
"cdna_start": 2723,
"cds_end": null,
"cds_length": 3009,
"cds_start": 2588,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000876334.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2588G>C",
"hgvs_p": "p.Arg863Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546393.1",
"strand": false,
"transcript": "ENST00000876334.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 993,
"aa_ref": "R",
"aa_start": 854,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4254,
"cdna_start": 2600,
"cds_end": null,
"cds_length": 2982,
"cds_start": 2561,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000876341.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2561G>C",
"hgvs_p": "p.Arg854Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546400.1",
"strand": false,
"transcript": "ENST00000876341.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 988,
"aa_ref": "R",
"aa_start": 849,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4307,
"cdna_start": 2653,
"cds_end": null,
"cds_length": 2967,
"cds_start": 2546,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000876339.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2546G>C",
"hgvs_p": "p.Arg849Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546398.1",
"strand": false,
"transcript": "ENST00000876339.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 985,
"aa_ref": "R",
"aa_start": 846,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4303,
"cdna_start": 2649,
"cds_end": null,
"cds_length": 2958,
"cds_start": 2537,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000876337.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2537G>C",
"hgvs_p": "p.Arg846Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546396.1",
"strand": false,
"transcript": "ENST00000876337.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 978,
"aa_ref": "R",
"aa_start": 886,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4282,
"cdna_start": 2769,
"cds_end": null,
"cds_length": 2937,
"cds_start": 2657,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000876336.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2657G>C",
"hgvs_p": "p.Arg886Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546395.1",
"strand": false,
"transcript": "ENST00000876336.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 953,
"aa_ref": "R",
"aa_start": 814,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4207,
"cdna_start": 2553,
"cds_end": null,
"cds_length": 2862,
"cds_start": 2441,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000876338.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2441G>C",
"hgvs_p": "p.Arg814Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546397.1",
"strand": false,
"transcript": "ENST00000876338.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 988,
"aa_ref": "R",
"aa_start": 849,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4337,
"cdna_start": 2683,
"cds_end": null,
"cds_length": 2967,
"cds_start": 2546,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "XM_017000507.2",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2546G>C",
"hgvs_p": "p.Arg849Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016855996.1",
"strand": false,
"transcript": "XM_017000507.2",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 953,
"aa_ref": "R",
"aa_start": 814,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4232,
"cdna_start": 2578,
"cds_end": null,
"cds_length": 2862,
"cds_start": 2441,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "XM_005270562.3",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2441G>C",
"hgvs_p": "p.Arg814Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005270619.2",
"strand": false,
"transcript": "XM_005270562.3",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 949,
"aa_ref": "R",
"aa_start": 810,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4341,
"cdna_start": 2687,
"cds_end": null,
"cds_length": 2850,
"cds_start": 2429,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "XM_047448076.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2429G>C",
"hgvs_p": "p.Arg810Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047304032.1",
"strand": false,
"transcript": "XM_047448076.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 916,
"aa_ref": "R",
"aa_start": 777,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4121,
"cdna_start": 2467,
"cds_end": null,
"cds_length": 2751,
"cds_start": 2330,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_047448077.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2330G>C",
"hgvs_p": "p.Arg777Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047304033.1",
"strand": false,
"transcript": "XM_047448077.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 533,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000422980.1",
"gene_hgnc_id": 40195,
"gene_symbol": "DPYD-AS1",
"hgvs_c": "n.64+2612C>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000422980.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 533,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_046590.1",
"gene_hgnc_id": 40195,
"gene_symbol": "DPYD-AS1",
"hgvs_c": "n.64+2612C>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_046590.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1801267",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 3.845,
"pos": 97098598,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.813,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000110.4"
}
]
}