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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: 1-153340507-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=153340507&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PGLYRP4",
"hgnc_id": 30015,
"hgvs_c": "c.698C>T",
"hgvs_p": "p.Ala233Val",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_020393.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_score": -4,
"allele_count_reference_population": 622,
"alphamissense_prediction": null,
"alphamissense_score": 0.1499,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.52,
"chr": "1",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.04068949818611145,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 373,
"aa_ref": "A",
"aa_start": 233,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2129,
"cdna_start": 1058,
"cds_end": null,
"cds_length": 1122,
"cds_start": 698,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_020393.4",
"gene_hgnc_id": 30015,
"gene_symbol": "PGLYRP4",
"hgvs_c": "c.698C>T",
"hgvs_p": "p.Ala233Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000359650.10",
"protein_coding": true,
"protein_id": "NP_065126.2",
"strand": false,
"transcript": "NM_020393.4",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 373,
"aa_ref": "A",
"aa_start": 233,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2129,
"cdna_start": 1058,
"cds_end": null,
"cds_length": 1122,
"cds_start": 698,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000359650.10",
"gene_hgnc_id": 30015,
"gene_symbol": "PGLYRP4",
"hgvs_c": "c.698C>T",
"hgvs_p": "p.Ala233Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_020393.4",
"protein_coding": true,
"protein_id": "ENSP00000352672.5",
"strand": false,
"transcript": "ENST00000359650.10",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 369,
"aa_ref": "A",
"aa_start": 229,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2116,
"cdna_start": 1045,
"cds_end": null,
"cds_length": 1110,
"cds_start": 686,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000368739.3",
"gene_hgnc_id": 30015,
"gene_symbol": "PGLYRP4",
"hgvs_c": "c.686C>T",
"hgvs_p": "p.Ala229Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000357728.3",
"strand": false,
"transcript": "ENST00000368739.3",
"transcript_support_level": 5
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 373,
"aa_ref": "A",
"aa_start": 233,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2138,
"cdna_start": 1067,
"cds_end": null,
"cds_length": 1122,
"cds_start": 698,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_011509789.3",
"gene_hgnc_id": 30015,
"gene_symbol": "PGLYRP4",
"hgvs_c": "c.698C>T",
"hgvs_p": "p.Ala233Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011508091.1",
"strand": false,
"transcript": "XM_011509789.3",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 373,
"aa_ref": "A",
"aa_start": 233,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1607,
"cdna_start": 1058,
"cds_end": null,
"cds_length": 1122,
"cds_start": 698,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_011509790.1",
"gene_hgnc_id": 30015,
"gene_symbol": "PGLYRP4",
"hgvs_c": "c.698C>T",
"hgvs_p": "p.Ala233Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011508092.1",
"strand": false,
"transcript": "XM_011509790.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 369,
"aa_ref": "A",
"aa_start": 229,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2117,
"cdna_start": 1046,
"cds_end": null,
"cds_length": 1110,
"cds_start": 686,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_011509791.3",
"gene_hgnc_id": 30015,
"gene_symbol": "PGLYRP4",
"hgvs_c": "c.686C>T",
"hgvs_p": "p.Ala229Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011508093.1",
"strand": false,
"transcript": "XM_011509791.3",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 340,
"aa_ref": "A",
"aa_start": 233,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1821,
"cdna_start": 1058,
"cds_end": null,
"cds_length": 1023,
"cds_start": 698,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_011509792.1",
"gene_hgnc_id": 30015,
"gene_symbol": "PGLYRP4",
"hgvs_c": "c.698C>T",
"hgvs_p": "p.Ala233Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011508094.1",
"strand": false,
"transcript": "XM_011509792.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 205,
"aa_ref": "A",
"aa_start": 65,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1817,
"cdna_start": 746,
"cds_end": null,
"cds_length": 618,
"cds_start": 194,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_011509793.2",
"gene_hgnc_id": 30015,
"gene_symbol": "PGLYRP4",
"hgvs_c": "c.194C>T",
"hgvs_p": "p.Ala65Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011508095.1",
"strand": false,
"transcript": "XM_011509793.2",
"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": 1827,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XR_007062001.1",
"gene_hgnc_id": 30015,
"gene_symbol": "PGLYRP4",
"hgvs_c": "n.1058C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "XR_007062001.1",
"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": 1522,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XR_921897.3",
"gene_hgnc_id": 30015,
"gene_symbol": "PGLYRP4",
"hgvs_c": "n.1058C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "XR_921897.3",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs138238733",
"effect": "missense_variant",
"frequency_reference_population": 0.00038534787,
"gene_hgnc_id": 30015,
"gene_symbol": "PGLYRP4",
"gnomad_exomes_ac": 581,
"gnomad_exomes_af": 0.000397437,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 41,
"gnomad_genomes_af": 0.00026928,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.359,
"pos": 153340507,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.138,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_020393.4"
}
]
}