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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: 1-15573706-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=15573706&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "AGMAT",
"hgnc_id": 18407,
"hgvs_c": "c.1004C>T",
"hgvs_p": "p.Ala335Val",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_024758.5",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "DNAJC16",
"hgnc_id": 29157,
"hgvs_c": "c.1950-1054G>A",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "ENST00000375849.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 31,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.7336,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.03,
"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": "Uncertain_significance",
"computational_score_selected": 0.4601857662200928,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 352,
"aa_ref": "A",
"aa_start": 335,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3095,
"cdna_start": 1088,
"cds_end": null,
"cds_length": 1059,
"cds_start": 1004,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_024758.5",
"gene_hgnc_id": 18407,
"gene_symbol": "AGMAT",
"hgvs_c": "c.1004C>T",
"hgvs_p": "p.Ala335Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000375826.4",
"protein_coding": true,
"protein_id": "NP_079034.3",
"strand": false,
"transcript": "NM_024758.5",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 352,
"aa_ref": "A",
"aa_start": 335,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3095,
"cdna_start": 1088,
"cds_end": null,
"cds_length": 1059,
"cds_start": 1004,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000375826.4",
"gene_hgnc_id": 18407,
"gene_symbol": "AGMAT",
"hgvs_c": "c.1004C>T",
"hgvs_p": "p.Ala335Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_024758.5",
"protein_coding": true,
"protein_id": "ENSP00000364986.3",
"strand": false,
"transcript": "ENST00000375826.4",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 655,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3446,
"cdna_start": null,
"cds_end": null,
"cds_length": 1968,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000375849.5",
"gene_hgnc_id": 29157,
"gene_symbol": "DNAJC16",
"hgvs_c": "c.1950-1054G>A",
"hgvs_p": null,
"intron_rank": 14,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000365009.1",
"strand": true,
"transcript": "ENST00000375849.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2847,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000483270.1",
"gene_hgnc_id": 29157,
"gene_symbol": "DNAJC16",
"hgvs_c": "n.2199-1054G>A",
"hgvs_p": null,
"intron_rank": 11,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000483270.1",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 349,
"aa_ref": "A",
"aa_start": 332,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1256,
"cdna_start": 1106,
"cds_end": null,
"cds_length": 1050,
"cds_start": 995,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000909207.1",
"gene_hgnc_id": 18407,
"gene_symbol": "AGMAT",
"hgvs_c": "c.995C>T",
"hgvs_p": "p.Ala332Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579266.1",
"strand": false,
"transcript": "ENST00000909207.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 292,
"aa_ref": "A",
"aa_start": 275,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1285,
"cdna_start": 894,
"cds_end": null,
"cds_length": 879,
"cds_start": 824,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000930536.1",
"gene_hgnc_id": 18407,
"gene_symbol": "AGMAT",
"hgvs_c": "c.824C>T",
"hgvs_p": "p.Ala275Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600595.1",
"strand": false,
"transcript": "ENST00000930536.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 159,
"aa_ref": "A",
"aa_start": 142,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 921,
"cdna_start": 536,
"cds_end": null,
"cds_length": 480,
"cds_start": 425,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000930535.1",
"gene_hgnc_id": 18407,
"gene_symbol": "AGMAT",
"hgvs_c": "c.425C>T",
"hgvs_p": "p.Ala142Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600594.1",
"strand": false,
"transcript": "ENST00000930535.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs202068651",
"effect": "missense_variant",
"frequency_reference_population": 0.000019205654,
"gene_hgnc_id": 18407,
"gene_symbol": "AGMAT",
"gnomad_exomes_ac": 27,
"gnomad_exomes_af": 0.0000184703,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 4,
"gnomad_genomes_af": 0.000026264,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.189,
"pos": 15573706,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.634,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_024758.5"
}
]
}