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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: 1-97098582-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=97098582&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 97098582,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_000110.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.2673A>G",
"hgvs_p": "p.Ala891Ala",
"transcript": "NM_000110.4",
"protein_id": "NP_000101.2",
"transcript_support_level": null,
"aa_start": 891,
"aa_end": null,
"aa_length": 1025,
"cds_start": 2673,
"cds_end": null,
"cds_length": 3078,
"cdna_start": 2785,
"cdna_end": null,
"cdna_length": 4423,
"mane_select": "ENST00000370192.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000110.4"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.2673A>G",
"hgvs_p": "p.Ala891Ala",
"transcript": "ENST00000370192.8",
"protein_id": "ENSP00000359211.3",
"transcript_support_level": 1,
"aa_start": 891,
"aa_end": null,
"aa_length": 1025,
"cds_start": 2673,
"cds_end": null,
"cds_length": 3078,
"cdna_start": 2785,
"cdna_end": null,
"cdna_length": 4423,
"mane_select": "NM_000110.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370192.8"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.2841A>G",
"hgvs_p": "p.Ala947Ala",
"transcript": "ENST00000876340.1",
"protein_id": "ENSP00000546399.1",
"transcript_support_level": null,
"aa_start": 947,
"aa_end": null,
"aa_length": 1081,
"cds_start": 2841,
"cds_end": null,
"cds_length": 3246,
"cdna_start": 2948,
"cdna_end": null,
"cdna_length": 4583,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876340.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.2778A>G",
"hgvs_p": "p.Ala926Ala",
"transcript": "ENST00000969915.1",
"protein_id": "ENSP00000639974.1",
"transcript_support_level": null,
"aa_start": 926,
"aa_end": null,
"aa_length": 1060,
"cds_start": 2778,
"cds_end": null,
"cds_length": 3183,
"cdna_start": 2890,
"cdna_end": null,
"cdna_length": 4525,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969915.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.2772A>G",
"hgvs_p": "p.Ala924Ala",
"transcript": "ENST00000876335.1",
"protein_id": "ENSP00000546394.1",
"transcript_support_level": null,
"aa_start": 924,
"aa_end": null,
"aa_length": 1058,
"cds_start": 2772,
"cds_end": null,
"cds_length": 3177,
"cdna_start": 2890,
"cdna_end": null,
"cdna_length": 4528,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876335.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.2673A>G",
"hgvs_p": "p.Ala891Ala",
"transcript": "ENST00000969914.1",
"protein_id": "ENSP00000639973.1",
"transcript_support_level": null,
"aa_start": 891,
"aa_end": null,
"aa_length": 1055,
"cds_start": 2673,
"cds_end": null,
"cds_length": 3168,
"cdna_start": 2803,
"cdna_end": null,
"cdna_length": 4527,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969914.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.2604A>G",
"hgvs_p": "p.Ala868Ala",
"transcript": "ENST00000876334.1",
"protein_id": "ENSP00000546393.1",
"transcript_support_level": null,
"aa_start": 868,
"aa_end": null,
"aa_length": 1002,
"cds_start": 2604,
"cds_end": null,
"cds_length": 3009,
"cdna_start": 2739,
"cdna_end": null,
"cdna_length": 4374,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876334.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.2577A>G",
"hgvs_p": "p.Ala859Ala",
"transcript": "ENST00000876341.1",
"protein_id": "ENSP00000546400.1",
"transcript_support_level": null,
"aa_start": 859,
"aa_end": null,
"aa_length": 993,
"cds_start": 2577,
"cds_end": null,
"cds_length": 2982,
"cdna_start": 2616,
"cdna_end": null,
"cdna_length": 4254,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876341.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.2562A>G",
"hgvs_p": "p.Ala854Ala",
"transcript": "ENST00000876339.1",
"protein_id": "ENSP00000546398.1",
"transcript_support_level": null,
"aa_start": 854,
"aa_end": null,
"aa_length": 988,
"cds_start": 2562,
"cds_end": null,
"cds_length": 2967,
"cdna_start": 2669,
"cdna_end": null,
"cdna_length": 4307,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876339.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.2553A>G",
"hgvs_p": "p.Ala851Ala",
"transcript": "ENST00000876337.1",
"protein_id": "ENSP00000546396.1",
"transcript_support_level": null,
"aa_start": 851,
"aa_end": null,
"aa_length": 985,
"cds_start": 2553,
"cds_end": null,
"cds_length": 2958,
"cdna_start": 2665,
"cdna_end": null,
"cdna_length": 4303,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876337.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.2673A>G",
"hgvs_p": "p.Ala891Ala",
"transcript": "ENST00000876336.1",
"protein_id": "ENSP00000546395.1",
"transcript_support_level": null,
"aa_start": 891,
"aa_end": null,
"aa_length": 978,
"cds_start": 2673,
"cds_end": null,
"cds_length": 2937,
"cdna_start": 2785,
"cdna_end": null,
"cdna_length": 4282,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876336.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.2457A>G",
"hgvs_p": "p.Ala819Ala",
"transcript": "ENST00000876338.1",
"protein_id": "ENSP00000546397.1",
"transcript_support_level": null,
"aa_start": 819,
"aa_end": null,
"aa_length": 953,
"cds_start": 2457,
"cds_end": null,
"cds_length": 2862,
"cdna_start": 2569,
"cdna_end": null,
"cdna_length": 4207,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876338.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.2562A>G",
"hgvs_p": "p.Ala854Ala",
"transcript": "XM_017000507.2",
"protein_id": "XP_016855996.1",
"transcript_support_level": null,
"aa_start": 854,
"aa_end": null,
"aa_length": 988,
"cds_start": 2562,
"cds_end": null,
"cds_length": 2967,
"cdna_start": 2699,
"cdna_end": null,
"cdna_length": 4337,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000507.2"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.2457A>G",
"hgvs_p": "p.Ala819Ala",
"transcript": "XM_005270562.3",
"protein_id": "XP_005270619.2",
"transcript_support_level": null,
"aa_start": 819,
"aa_end": null,
"aa_length": 953,
"cds_start": 2457,
"cds_end": null,
"cds_length": 2862,
"cdna_start": 2594,
"cdna_end": null,
"cdna_length": 4232,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005270562.3"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.2445A>G",
"hgvs_p": "p.Ala815Ala",
"transcript": "XM_047448076.1",
"protein_id": "XP_047304032.1",
"transcript_support_level": null,
"aa_start": 815,
"aa_end": null,
"aa_length": 949,
"cds_start": 2445,
"cds_end": null,
"cds_length": 2850,
"cdna_start": 2703,
"cdna_end": null,
"cdna_length": 4341,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448076.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"hgvs_c": "c.2346A>G",
"hgvs_p": "p.Ala782Ala",
"transcript": "XM_047448077.1",
"protein_id": "XP_047304033.1",
"transcript_support_level": null,
"aa_start": 782,
"aa_end": null,
"aa_length": 916,
"cds_start": 2346,
"cds_end": null,
"cds_length": 2751,
"cdna_start": 2483,
"cdna_end": null,
"cdna_length": 4121,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448077.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "DPYD-AS1",
"gene_hgnc_id": 40195,
"hgvs_c": "n.64+2596T>C",
"hgvs_p": null,
"transcript": "ENST00000422980.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 533,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000422980.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "DPYD-AS1",
"gene_hgnc_id": 40195,
"hgvs_c": "n.64+2596T>C",
"hgvs_p": null,
"transcript": "NR_046590.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 533,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_046590.1"
}
],
"gene_symbol": "DPYD",
"gene_hgnc_id": 3012,
"dbsnp": "rs376391343",
"frequency_reference_population": 0.000027274576,
"hom_count_reference_population": 0,
"allele_count_reference_population": 44,
"gnomad_exomes_af": 0.0000116362,
"gnomad_genomes_af": 0.000177324,
"gnomad_exomes_ac": 17,
"gnomad_genomes_ac": 27,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5199999809265137,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.52,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.332,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP6,BP7",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_000110.4",
"gene_symbol": "DPYD",
"hgnc_id": 3012,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2673A>G",
"hgvs_p": "p.Ala891Ala"
},
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000422980.1",
"gene_symbol": "DPYD-AS1",
"hgnc_id": 40195,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.64+2596T>C",
"hgvs_p": null
}
],
"clinvar_disease": "DPYD-related disorder",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "DPYD-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}