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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: 1-97921165-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=97921165&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "DPYD",
"hgnc_id": 3012,
"hgvs_c": "n.688+20408G>C",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "ENST00000646851.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.82,
"chr": "1",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.8199999928474426,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 799,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000646851.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "n.688+20408G>C",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000646851.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1025,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4423,
"cdna_start": null,
"cds_end": null,
"cds_length": 3078,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 23,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_000110.4",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.-243G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000370192.8",
"protein_coding": true,
"protein_id": "NP_000101.2",
"strand": true,
"transcript": "NM_000110.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1025,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4423,
"cdna_start": null,
"cds_end": null,
"cds_length": 3078,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 23,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000370192.8",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.-243G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000110.4",
"protein_coding": true,
"protein_id": "ENSP00000359211.3",
"strand": true,
"transcript": "ENST00000370192.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 173,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1779,
"cdna_start": null,
"cds_end": null,
"cds_length": 522,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000306031.5",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.-243G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000307107.5",
"strand": true,
"transcript": "ENST00000306031.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1081,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4583,
"cdna_start": null,
"cds_end": null,
"cds_length": 3246,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 24,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000876340.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.-243G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546399.1",
"strand": true,
"transcript": "ENST00000876340.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1060,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4525,
"cdna_start": null,
"cds_end": null,
"cds_length": 3183,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 24,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000969915.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.-243G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000639974.1",
"strand": true,
"transcript": "ENST00000969915.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1058,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4528,
"cdna_start": null,
"cds_end": null,
"cds_length": 3177,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 24,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000876335.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.-243G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546394.1",
"strand": true,
"transcript": "ENST00000876335.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1055,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4527,
"cdna_start": null,
"cds_end": null,
"cds_length": 3168,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 24,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000969914.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.-243G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000639973.1",
"strand": true,
"transcript": "ENST00000969914.1",
"transcript_support_level": null
},
{
"aa_alt": null,
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"aa_length": 1002,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4374,
"cdna_start": null,
"cds_end": null,
"cds_length": 3009,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000876334.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.-243G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546393.1",
"strand": true,
"transcript": "ENST00000876334.1",
"transcript_support_level": null
},
{
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"aa_length": 993,
"aa_ref": null,
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4254,
"cdna_start": null,
"cds_end": null,
"cds_length": 2982,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 23,
"exon_rank": null,
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"feature": "ENST00000876341.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.-243G>C",
"hgvs_p": null,
"intron_rank": null,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000546400.1",
"strand": true,
"transcript": "ENST00000876341.1",
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},
{
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"consequences": [
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],
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"feature": "ENST00000876339.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000546398.1",
"strand": true,
"transcript": "ENST00000876339.1",
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},
{
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"consequences": [
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],
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"feature": "ENST00000876337.1",
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"protein_coding": true,
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"strand": true,
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},
{
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],
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"feature": "ENST00000876336.1",
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},
{
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"cdna_start": null,
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"consequences": [
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],
"exon_count": 22,
"exon_rank": null,
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"feature": "ENST00000876338.1",
"gene_hgnc_id": 3012,
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"hgvs_c": "c.-243G>C",
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000546397.1",
"strand": true,
"transcript": "ENST00000876338.1",
"transcript_support_level": null
},
{
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"consequences": [
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],
"exon_count": 6,
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"feature": "NM_001160301.1",
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"protein_coding": true,
"protein_id": "NP_001153773.1",
"strand": true,
"transcript": "NM_001160301.1",
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},
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"consequences": [
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],
"exon_count": 22,
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"feature": "XM_017000507.2",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.-243G>C",
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "XP_016855996.1",
"strand": true,
"transcript": "XM_017000507.2",
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},
{
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"consequences": [
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],
"exon_count": 22,
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"feature": "XM_005270562.3",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.-243G>C",
"hgvs_p": null,
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"protein_coding": true,
"protein_id": "XP_005270619.2",
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"transcript": "XM_005270562.3",
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},
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"consequences": [
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],
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"feature": "XM_047448077.1",
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},
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"consequences": [
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],
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"feature": "XM_006710397.4",
"gene_hgnc_id": 3012,
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"hgvs_c": "c.-243G>C",
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"protein_id": "XP_006710460.1",
"strand": true,
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},
{
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"biotype": "pseudogene",
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"consequences": [
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],
"exon_count": 3,
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"feature": "ENST00000460019.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "n.-168G>C",
"hgvs_p": null,
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"mane_plus": null,
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"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000460019.1",
"transcript_support_level": 2
},
{
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"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
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"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_001737014.2",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "n.-106G>C",
"hgvs_p": null,
"intron_rank": null,
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"mane_plus": null,
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"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_001737014.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs72981743",
"effect": "intron_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"gnomad_exomes_ac": 0,
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}
]
}