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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: 1-97691806-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=97691806&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 97691806,
"ref": "G",
"alt": "A",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000370192.8",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.681-8C>T",
"hgvs_p": null,
"transcript": "NM_000110.4",
"protein_id": "NP_000101.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1025,
"cds_start": -4,
"cds_end": null,
"cds_length": 3078,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4423,
"mane_select": "ENST00000370192.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.681-8C>T",
"hgvs_p": null,
"transcript": "ENST00000370192.8",
"protein_id": "ENSP00000359211.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1025,
"cds_start": -4,
"cds_end": null,
"cds_length": 3078,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4423,
"mane_select": "NM_000110.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "n.445-8C>T",
"hgvs_p": null,
"transcript": "ENST00000474241.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 1036,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.570-8C>T",
"hgvs_p": null,
"transcript": "XM_017000507.2",
"protein_id": "XP_016855996.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 988,
"cds_start": -4,
"cds_end": null,
"cds_length": 2967,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4337,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.681-8C>T",
"hgvs_p": null,
"transcript": "XM_005270562.3",
"protein_id": "XP_005270619.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 953,
"cds_start": -4,
"cds_end": null,
"cds_length": 2862,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4232,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.453-8C>T",
"hgvs_p": null,
"transcript": "XM_047448076.1",
"protein_id": "XP_047304032.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 949,
"cds_start": -4,
"cds_end": null,
"cds_length": 2850,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4341,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.570-8C>T",
"hgvs_p": null,
"transcript": "XM_047448077.1",
"protein_id": "XP_047304033.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 916,
"cds_start": -4,
"cds_end": null,
"cds_length": 2751,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4121,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.681-8C>T",
"hgvs_p": null,
"transcript": "XM_006710397.4",
"protein_id": "XP_006710460.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 889,
"cds_start": -4,
"cds_end": null,
"cds_length": 2670,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3097,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"dbsnp": "rs74774246",
"frequency_reference_population": 0.00241207,
"hom_count_reference_population": 78,
"allele_count_reference_population": 3889,
"gnomad_exomes_af": 0.00138611,
"gnomad_genomes_af": 0.0122609,
"gnomad_exomes_ac": 2024,
"gnomad_genomes_ac": 1865,
"gnomad_exomes_homalt": 44,
"gnomad_genomes_homalt": 34,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8899999856948853,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.004000000189989805,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.89,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.056,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000216759150002593,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000370192.8",
"gene_symbol": "DPYD",
"hgnc_id": 3012,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.681-8C>T",
"hgvs_p": null
}
],
"clinvar_disease": "DPYD-related disorder,Dihydropyrimidine dehydrogenase deficiency,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:2",
"phenotype_combined": "not provided|Dihydropyrimidine dehydrogenase deficiency|DPYD-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}