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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: 20-5118827-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=5118827&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 5118827,
"ref": "G",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_002592.2",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNA",
"gene_hgnc_id": 8729,
"hgvs_c": "c.261C>A",
"hgvs_p": "p.Ile87Ile",
"transcript": "NM_182649.2",
"protein_id": "NP_872590.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 261,
"cds_start": 261,
"cds_end": null,
"cds_length": 786,
"cdna_start": 421,
"cdna_end": null,
"cdna_length": 1276,
"mane_select": "ENST00000379143.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_182649.2"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNA",
"gene_hgnc_id": 8729,
"hgvs_c": "c.261C>A",
"hgvs_p": "p.Ile87Ile",
"transcript": "ENST00000379143.10",
"protein_id": "ENSP00000368438.5",
"transcript_support_level": 1,
"aa_start": 87,
"aa_end": null,
"aa_length": 261,
"cds_start": 261,
"cds_end": null,
"cds_length": 786,
"cdna_start": 421,
"cdna_end": null,
"cdna_length": 1276,
"mane_select": "NM_182649.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000379143.10"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNA",
"gene_hgnc_id": 8729,
"hgvs_c": "c.261C>A",
"hgvs_p": "p.Ile87Ile",
"transcript": "NM_002592.2",
"protein_id": "NP_002583.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 261,
"cds_start": 261,
"cds_end": null,
"cds_length": 786,
"cdna_start": 500,
"cdna_end": null,
"cdna_length": 1355,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002592.2"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNA",
"gene_hgnc_id": 8729,
"hgvs_c": "c.261C>A",
"hgvs_p": "p.Ile87Ile",
"transcript": "ENST00000379160.3",
"protein_id": "ENSP00000368458.3",
"transcript_support_level": 5,
"aa_start": 87,
"aa_end": null,
"aa_length": 261,
"cds_start": 261,
"cds_end": null,
"cds_length": 786,
"cdna_start": 504,
"cdna_end": null,
"cdna_length": 1359,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000379160.3"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNA",
"gene_hgnc_id": 8729,
"hgvs_c": "c.261C>A",
"hgvs_p": "p.Ile87Ile",
"transcript": "ENST00000875657.1",
"protein_id": "ENSP00000545716.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 261,
"cds_start": 261,
"cds_end": null,
"cds_length": 786,
"cdna_start": 410,
"cdna_end": null,
"cdna_length": 1265,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875657.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNA",
"gene_hgnc_id": 8729,
"hgvs_c": "c.261C>A",
"hgvs_p": "p.Ile87Ile",
"transcript": "ENST00000968046.1",
"protein_id": "ENSP00000638105.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 261,
"cds_start": 261,
"cds_end": null,
"cds_length": 786,
"cdna_start": 409,
"cdna_end": null,
"cdna_length": 1262,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000968046.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNA",
"gene_hgnc_id": 8729,
"hgvs_c": "c.261C>A",
"hgvs_p": "p.Ile87Ile",
"transcript": "ENST00000875656.1",
"protein_id": "ENSP00000545715.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 259,
"cds_start": 261,
"cds_end": null,
"cds_length": 780,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 1329,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875656.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNA",
"gene_hgnc_id": 8729,
"hgvs_c": "c.261C>A",
"hgvs_p": "p.Ile87Ile",
"transcript": "ENST00000875658.1",
"protein_id": "ENSP00000545717.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 259,
"cds_start": 261,
"cds_end": null,
"cds_length": 780,
"cdna_start": 475,
"cdna_end": null,
"cdna_length": 1324,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875658.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNA",
"gene_hgnc_id": 8729,
"hgvs_c": "c.261C>A",
"hgvs_p": "p.Ile87Ile",
"transcript": "ENST00000875659.1",
"protein_id": "ENSP00000545718.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 259,
"cds_start": 261,
"cds_end": null,
"cds_length": 780,
"cdna_start": 454,
"cdna_end": null,
"cdna_length": 1303,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875659.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNA",
"gene_hgnc_id": 8729,
"hgvs_c": "c.261C>A",
"hgvs_p": "p.Ile87Ile",
"transcript": "ENST00000968047.1",
"protein_id": "ENSP00000638106.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 259,
"cds_start": 261,
"cds_end": null,
"cds_length": 780,
"cdna_start": 462,
"cdna_end": null,
"cdna_length": 1303,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000968047.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNA",
"gene_hgnc_id": 8729,
"hgvs_c": "c.261C>A",
"hgvs_p": "p.Ile87Ile",
"transcript": "ENST00000930445.1",
"protein_id": "ENSP00000600504.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 256,
"cds_start": 261,
"cds_end": null,
"cds_length": 771,
"cdna_start": 418,
"cdna_end": null,
"cdna_length": 1253,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930445.1"
}
],
"gene_symbol": "PCNA",
"gene_hgnc_id": 8729,
"dbsnp": "rs142530566",
"frequency_reference_population": 0.00002912352,
"hom_count_reference_population": 0,
"allele_count_reference_population": 47,
"gnomad_exomes_af": 0.0000164211,
"gnomad_genomes_af": 0.000151034,
"gnomad_exomes_ac": 24,
"gnomad_genomes_ac": 23,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.4699999988079071,
"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": -0.47,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.859,
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Benign",
"transcript": "NM_002592.2",
"gene_symbol": "PCNA",
"hgnc_id": 8729,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.261C>A",
"hgvs_p": "p.Ile87Ile"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}