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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: 12-55902070-AG-GA (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=55902070&ref=AG&alt=GA&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [],
"effects": [
"missense_variant"
],
"gene_symbol": "PYM1",
"hgnc_id": 30258,
"hgvs_c": "c.416_417delCTinsTC",
"hgvs_p": "p.Ser139Phe",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": 0,
"transcript": "NM_032345.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_score": 0,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "GA",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "12",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 204,
"aa_ref": "S",
"aa_start": 139,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1207,
"cdna_start": 550,
"cds_end": null,
"cds_length": 615,
"cds_start": 416,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_032345.3",
"gene_hgnc_id": 30258,
"gene_symbol": "PYM1",
"hgvs_c": "c.416_417delCTinsTC",
"hgvs_p": "p.Ser139Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000408946.7",
"protein_coding": true,
"protein_id": "NP_115721.1",
"strand": false,
"transcript": "NM_032345.3",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 204,
"aa_ref": "S",
"aa_start": 139,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1207,
"cdna_start": 550,
"cds_end": null,
"cds_length": 615,
"cds_start": 416,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000408946.7",
"gene_hgnc_id": 30258,
"gene_symbol": "PYM1",
"hgvs_c": "c.416_417delCTinsTC",
"hgvs_p": "p.Ser139Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_032345.3",
"protein_coding": true,
"protein_id": "ENSP00000386156.2",
"strand": false,
"transcript": "ENST00000408946.7",
"transcript_support_level": 1
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 203,
"aa_ref": "S",
"aa_start": 138,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1087,
"cdna_start": 430,
"cds_end": null,
"cds_length": 612,
"cds_start": 413,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001143853.1",
"gene_hgnc_id": 30258,
"gene_symbol": "PYM1",
"hgvs_c": "c.413_414delCTinsTC",
"hgvs_p": "p.Ser138Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001137325.1",
"strand": false,
"transcript": "NM_001143853.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 203,
"aa_ref": "S",
"aa_start": 138,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1073,
"cdna_start": 417,
"cds_end": null,
"cds_length": 612,
"cds_start": 413,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000398213.4",
"gene_hgnc_id": 30258,
"gene_symbol": "PYM1",
"hgvs_c": "c.413_414delCTinsTC",
"hgvs_p": "p.Ser138Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000381271.4",
"strand": false,
"transcript": "ENST00000398213.4",
"transcript_support_level": 2
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 173,
"aa_ref": "S",
"aa_start": 108,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1108,
"cdna_start": 453,
"cds_end": null,
"cds_length": 522,
"cds_start": 323,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000859965.1",
"gene_hgnc_id": 30258,
"gene_symbol": "PYM1",
"hgvs_c": "c.323_324delCTinsTC",
"hgvs_p": "p.Ser108Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000530024.1",
"strand": false,
"transcript": "ENST00000859965.1",
"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": 890,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000302533.6",
"gene_hgnc_id": 30258,
"gene_symbol": "PYM1",
"hgvs_c": "n.506_507delCTinsTC",
"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": "ENST00000302533.6",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 499,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000547925.1",
"gene_hgnc_id": 30258,
"gene_symbol": "PYM1",
"hgvs_c": "n.469_470delCTinsTC",
"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": "ENST00000547925.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 775,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000557259.5",
"gene_hgnc_id": 30258,
"gene_symbol": "PYM1",
"hgvs_c": "n.675_676delCTinsTC",
"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": "ENST00000557259.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": null,
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 30258,
"gene_symbol": "PYM1",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.419,
"pos": 55902070,
"ref": "AG",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": null,
"splice_score_selected": null,
"splice_source_selected": null,
"spliceai_max_prediction": null,
"spliceai_max_score": null,
"transcript": "NM_032345.3"
}
]
}