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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: 5-60161151-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=60161151&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 60161151,
"ref": "C",
"alt": "T",
"effect": "intron_variant",
"transcript": "NM_001165899.2",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PDE4D",
"gene_hgnc_id": 8783,
"hgvs_c": "c.42+24406G>A",
"hgvs_p": null,
"transcript": "ENST00000502484.6",
"protein_id": "ENSP00000423094.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 748,
"cds_start": -4,
"cds_end": null,
"cds_length": 2247,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2478,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PDE4D",
"gene_hgnc_id": 8783,
"hgvs_c": "n.288+24406G>A",
"hgvs_p": null,
"transcript": "ENST00000509355.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 847,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PDE4D",
"gene_hgnc_id": 8783,
"hgvs_c": "n.43-334G>A",
"hgvs_p": null,
"transcript": "ENST00000509368.6",
"protein_id": "ENSP00000423555.2",
"transcript_support_level": 1,
"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": 2809,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PDE4D",
"gene_hgnc_id": 8783,
"hgvs_c": "c.42+24406G>A",
"hgvs_p": null,
"transcript": "NM_001165899.2",
"protein_id": "NP_001159371.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 748,
"cds_start": -4,
"cds_end": null,
"cds_length": 2247,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8086,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PDE4D",
"gene_hgnc_id": 8783,
"hgvs_c": "c.42+24406G>A",
"hgvs_p": null,
"transcript": "NM_001364599.1",
"protein_id": "NP_001351528.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 748,
"cds_start": -4,
"cds_end": null,
"cds_length": 2247,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8110,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PDE4D",
"gene_hgnc_id": 8783,
"hgvs_c": "c.-62+24406G>A",
"hgvs_p": null,
"transcript": "NM_001349241.2",
"protein_id": "NP_001336170.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 738,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 2,
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"gene_symbol": "PDE4D",
"gene_hgnc_id": 8783,
"hgvs_c": "c.-543+24406G>A",
"hgvs_p": null,
"transcript": "NM_001349243.2",
"protein_id": "NP_001336172.1",
"transcript_support_level": null,
"aa_start": null,
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"cdna_start": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PDE4D",
"gene_hgnc_id": 8783,
"hgvs_c": "c.42+24406G>A",
"hgvs_p": null,
"transcript": "NM_001364600.2",
"protein_id": "NP_001351529.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 222,
"cds_start": -4,
"cds_end": null,
"cds_length": 669,
"cdna_start": null,
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"cdna_length": 1487,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PDE4D",
"gene_hgnc_id": 8783,
"hgvs_c": "c.42+24406G>A",
"hgvs_p": null,
"transcript": "ENST00000505507.6",
"protein_id": "ENSP00000425910.2",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 80,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"feature": null
},
{
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],
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"transcript": "ENST00000514552.5",
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},
{
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],
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"gene_symbol": "PDE4D",
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"transcript": "ENST00000515835.2",
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],
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],
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}
],
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"dbsnp": "rs2962975",
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"gnomad_genomes_af": 0.674921,
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"gnomad_genomes_ac": 102538,
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"gnomad_genomes_homalt": 35152,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8299999833106995,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
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"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.83,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.568,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
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"acmg_score": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_001165899.2",
"gene_symbol": "PDE4D",
"hgnc_id": 8783,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.42+24406G>A",
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}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}