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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: 9-76184650-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=76184650&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"intron_variant"
],
"gene_symbol": "PCSK5",
"hgnc_id": 8747,
"hgvs_c": "c.2198-23C>T",
"hgvs_p": null,
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -12,
"transcript": "NM_001372043.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_score": -12,
"allele_count_reference_population": 1492542,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.73,
"chr": "9",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.7300000190734863,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1887,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10226,
"cdna_start": null,
"cds_end": null,
"cds_length": 5664,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 38,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001372043.1",
"gene_hgnc_id": 8747,
"gene_symbol": "PCSK5",
"hgvs_c": "c.2198-23C>T",
"hgvs_p": null,
"intron_rank": 16,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000674117.1",
"protein_coding": true,
"protein_id": "NP_001358972.1",
"strand": true,
"transcript": "NM_001372043.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1887,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 10226,
"cdna_start": null,
"cds_end": null,
"cds_length": 5664,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 38,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000674117.1",
"gene_hgnc_id": 8747,
"gene_symbol": "PCSK5",
"hgvs_c": "c.2198-23C>T",
"hgvs_p": null,
"intron_rank": 16,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001372043.1",
"protein_coding": true,
"protein_id": "ENSP00000500971.1",
"strand": true,
"transcript": "ENST00000674117.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 913,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5788,
"cdna_start": null,
"cds_end": null,
"cds_length": 2742,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 21,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000376752.9",
"gene_hgnc_id": 8747,
"gene_symbol": "PCSK5",
"hgvs_c": "c.2198-23C>T",
"hgvs_p": null,
"intron_rank": 16,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000365943.4",
"strand": true,
"transcript": "ENST00000376752.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1886,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7143,
"cdna_start": null,
"cds_end": null,
"cds_length": 5661,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 38,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000854198.1",
"gene_hgnc_id": 8747,
"gene_symbol": "PCSK5",
"hgvs_c": "c.2198-23C>T",
"hgvs_p": null,
"intron_rank": 16,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000524257.1",
"strand": true,
"transcript": "ENST00000854198.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1860,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10145,
"cdna_start": null,
"cds_end": null,
"cds_length": 5583,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 37,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001190482.2",
"gene_hgnc_id": 8747,
"gene_symbol": "PCSK5",
"hgvs_c": "c.2198-23C>T",
"hgvs_p": null,
"intron_rank": 16,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001177411.1",
"strand": true,
"transcript": "NM_001190482.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1860,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9538,
"cdna_start": null,
"cds_end": null,
"cds_length": 5583,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 37,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000545128.5",
"gene_hgnc_id": 8747,
"gene_symbol": "PCSK5",
"hgvs_c": "c.2198-23C>T",
"hgvs_p": null,
"intron_rank": 16,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000446280.1",
"strand": true,
"transcript": "ENST00000545128.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1560,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4731,
"cdna_start": null,
"cds_end": null,
"cds_length": 4683,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 31,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000424854.6",
"gene_hgnc_id": 8747,
"gene_symbol": "PCSK5",
"hgvs_c": "c.1217-23C>T",
"hgvs_p": null,
"intron_rank": 9,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000411654.1",
"strand": true,
"transcript": "ENST00000424854.6",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 913,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5788,
"cdna_start": null,
"cds_end": null,
"cds_length": 2742,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 21,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_006200.6",
"gene_hgnc_id": 8747,
"gene_symbol": "PCSK5",
"hgvs_c": "c.2198-23C>T",
"hgvs_p": null,
"intron_rank": 16,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_006191.2",
"strand": true,
"transcript": "NM_006200.6",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1886,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10223,
"cdna_start": null,
"cds_end": null,
"cds_length": 5661,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 38,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011518769.4",
"gene_hgnc_id": 8747,
"gene_symbol": "PCSK5",
"hgvs_c": "c.2198-23C>T",
"hgvs_p": null,
"intron_rank": 16,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011517071.1",
"strand": true,
"transcript": "XM_011518769.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1792,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9995,
"cdna_start": null,
"cds_end": null,
"cds_length": 5379,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 38,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047423454.1",
"gene_hgnc_id": 8747,
"gene_symbol": "PCSK5",
"hgvs_c": "c.1913-23C>T",
"hgvs_p": null,
"intron_rank": 16,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047279410.1",
"strand": true,
"transcript": "XM_047423454.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1441,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13071,
"cdna_start": null,
"cds_end": null,
"cds_length": 4326,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 29,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011518770.3",
"gene_hgnc_id": 8747,
"gene_symbol": "PCSK5",
"hgvs_c": "c.860-23C>T",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011517072.1",
"strand": true,
"transcript": "XM_011518770.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 885,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4574,
"cdna_start": null,
"cds_end": null,
"cds_length": 2658,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 21,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047423455.1",
"gene_hgnc_id": 8747,
"gene_symbol": "PCSK5",
"hgvs_c": "c.2198-23C>T",
"hgvs_p": null,
"intron_rank": 16,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047279411.1",
"strand": true,
"transcript": "XM_047423455.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 814,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3050,
"cdna_start": null,
"cds_end": null,
"cds_length": 2445,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 19,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047423456.1",
"gene_hgnc_id": 8747,
"gene_symbol": "PCSK5",
"hgvs_c": "c.2197+3059C>T",
"hgvs_p": null,
"intron_rank": 16,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047279412.1",
"strand": true,
"transcript": "XM_047423456.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 5684,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 20,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_120409.2",
"gene_hgnc_id": 8747,
"gene_symbol": "PCSK5",
"hgvs_c": "n.2603-23C>T",
"hgvs_p": null,
"intron_rank": 15,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_120409.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1537183",
"effect": "intron_variant",
"frequency_reference_population": 0.9732277,
"gene_hgnc_id": 8747,
"gene_symbol": "PCSK5",
"gnomad_exomes_ac": 1343533,
"gnomad_exomes_af": 0.972679,
"gnomad_exomes_homalt": 653552,
"gnomad_genomes_ac": 149009,
"gnomad_genomes_af": 0.978199,
"gnomad_genomes_homalt": 72897,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 726449,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.65,
"pos": 76184650,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001372043.1"
}
]
}