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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: 1-97234916-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=97234916&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PP3",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "DPYD",
"hgnc_id": 3012,
"hgvs_c": "c.2378C>T",
"hgvs_p": "p.Thr793Ile",
"inheritance_mode": "AR",
"pathogenic_score": 1,
"score": -3,
"transcript": "NM_000110.4",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"PP3",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "DPYD-AS1",
"hgnc_id": 40195,
"hgvs_c": "n.65-30498G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 1,
"score": -3,
"transcript": "ENST00000422980.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3,BS2",
"acmg_score": -3,
"allele_count_reference_population": 48,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.7387,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.2,
"chr": "1",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Dihydropyrimidine dehydrogenase deficiency,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:4",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.7956551313400269,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 1025,
"aa_ref": "T",
"aa_start": 793,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4423,
"cdna_start": 2490,
"cds_end": null,
"cds_length": 3078,
"cds_start": 2378,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "NM_000110.4",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2378C>T",
"hgvs_p": "p.Thr793Ile",
"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": "I",
"aa_end": null,
"aa_length": 1025,
"aa_ref": "T",
"aa_start": 793,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4423,
"cdna_start": 2490,
"cds_end": null,
"cds_length": 3078,
"cds_start": 2378,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000370192.8",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2378C>T",
"hgvs_p": "p.Thr793Ile",
"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": "I",
"aa_end": null,
"aa_length": 1081,
"aa_ref": "T",
"aa_start": 849,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4583,
"cdna_start": 2653,
"cds_end": null,
"cds_length": 3246,
"cds_start": 2546,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000876340.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2546C>T",
"hgvs_p": "p.Thr849Ile",
"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": "I",
"aa_end": null,
"aa_length": 1060,
"aa_ref": "T",
"aa_start": 793,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4525,
"cdna_start": 2490,
"cds_end": null,
"cds_length": 3183,
"cds_start": 2378,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000969915.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2378C>T",
"hgvs_p": "p.Thr793Ile",
"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": "I",
"aa_end": null,
"aa_length": 1058,
"aa_ref": "T",
"aa_start": 826,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4528,
"cdna_start": 2595,
"cds_end": null,
"cds_length": 3177,
"cds_start": 2477,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000876335.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2477C>T",
"hgvs_p": "p.Thr826Ile",
"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": "I",
"aa_end": null,
"aa_length": 1055,
"aa_ref": "T",
"aa_start": 793,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4527,
"cdna_start": 2508,
"cds_end": null,
"cds_length": 3168,
"cds_start": 2378,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000969914.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2378C>T",
"hgvs_p": "p.Thr793Ile",
"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": "I",
"aa_end": null,
"aa_length": 1002,
"aa_ref": "T",
"aa_start": 770,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4374,
"cdna_start": 2444,
"cds_end": null,
"cds_length": 3009,
"cds_start": 2309,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000876334.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2309C>T",
"hgvs_p": "p.Thr770Ile",
"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": "I",
"aa_end": null,
"aa_length": 993,
"aa_ref": "T",
"aa_start": 761,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4254,
"cdna_start": 2321,
"cds_end": null,
"cds_length": 2982,
"cds_start": 2282,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000876341.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2282C>T",
"hgvs_p": "p.Thr761Ile",
"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": "I",
"aa_end": null,
"aa_length": 988,
"aa_ref": "T",
"aa_start": 756,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4307,
"cdna_start": 2374,
"cds_end": null,
"cds_length": 2967,
"cds_start": 2267,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000876339.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2267C>T",
"hgvs_p": "p.Thr756Ile",
"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": "I",
"aa_end": null,
"aa_length": 985,
"aa_ref": "T",
"aa_start": 753,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4303,
"cdna_start": 2370,
"cds_end": null,
"cds_length": 2958,
"cds_start": 2258,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000876337.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2258C>T",
"hgvs_p": "p.Thr753Ile",
"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": "I",
"aa_end": null,
"aa_length": 978,
"aa_ref": "T",
"aa_start": 793,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4282,
"cdna_start": 2490,
"cds_end": null,
"cds_length": 2937,
"cds_start": 2378,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000876336.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2378C>T",
"hgvs_p": "p.Thr793Ile",
"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": "I",
"aa_end": null,
"aa_length": 953,
"aa_ref": "T",
"aa_start": 721,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4207,
"cdna_start": 2274,
"cds_end": null,
"cds_length": 2862,
"cds_start": 2162,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000876338.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2162C>T",
"hgvs_p": "p.Thr721Ile",
"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": "I",
"aa_end": null,
"aa_length": 988,
"aa_ref": "T",
"aa_start": 756,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4337,
"cdna_start": 2404,
"cds_end": null,
"cds_length": 2967,
"cds_start": 2267,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "XM_017000507.2",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2267C>T",
"hgvs_p": "p.Thr756Ile",
"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": "I",
"aa_end": null,
"aa_length": 953,
"aa_ref": "T",
"aa_start": 721,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4232,
"cdna_start": 2299,
"cds_end": null,
"cds_length": 2862,
"cds_start": 2162,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "XM_005270562.3",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2162C>T",
"hgvs_p": "p.Thr721Ile",
"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": "I",
"aa_end": null,
"aa_length": 949,
"aa_ref": "T",
"aa_start": 717,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4341,
"cdna_start": 2408,
"cds_end": null,
"cds_length": 2850,
"cds_start": 2150,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_047448076.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2150C>T",
"hgvs_p": "p.Thr717Ile",
"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": "I",
"aa_end": null,
"aa_length": 916,
"aa_ref": "T",
"aa_start": 684,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4121,
"cdna_start": 2188,
"cds_end": null,
"cds_length": 2751,
"cds_start": 2051,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "XM_047448077.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2051C>T",
"hgvs_p": "p.Thr684Ile",
"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": "I",
"aa_end": null,
"aa_length": 889,
"aa_ref": "T",
"aa_start": 793,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3097,
"cdna_start": 2515,
"cds_end": null,
"cds_length": 2670,
"cds_start": 2378,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_006710397.4",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2378C>T",
"hgvs_p": "p.Thr793Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006710460.1",
"strand": false,
"transcript": "XM_006710397.4",
"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.65-30498G>A",
"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.65-30498G>A",
"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": "rs547099198",
"effect": "missense_variant",
"frequency_reference_population": 0.000029740957,
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"gnomad_exomes_ac": 43,
"gnomad_exomes_af": 0.0000294159,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_ac": 5,
"gnomad_genomes_af": 0.000032864,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 2,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Dihydropyrimidine dehydrogenase deficiency|not specified|not provided",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.602,
"pos": 97234916,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.724,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
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