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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: X-48059483-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=48059483&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"BP4_Moderate",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ZNF630",
"hgnc_id": 28855,
"hgvs_c": "c.959A>T",
"hgvs_p": "p.Glu320Val",
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -6,
"transcript": "NM_001037735.4",
"verdict": "Likely_benign"
},
{
"benign_score": 6,
"criteria": [
"BP4_Moderate",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ZNF630-AS1",
"hgnc_id": 41215,
"hgvs_c": "n.123+3051T>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -6,
"transcript": "ENST00000614448.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_score": -6,
"allele_count_reference_population": 30,
"alphamissense_prediction": null,
"alphamissense_score": 0.1356,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.72,
"chr": "X",
"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": 0.08803430199623108,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 657,
"aa_ref": "E",
"aa_start": 320,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3475,
"cdna_start": 1508,
"cds_end": null,
"cds_length": 1974,
"cds_start": 959,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001282201.2",
"gene_hgnc_id": 28855,
"gene_symbol": "ZNF630",
"hgvs_c": "c.959A>T",
"hgvs_p": "p.Glu320Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000276054.9",
"protein_coding": true,
"protein_id": "NP_001269130.1",
"strand": false,
"transcript": "NM_001282201.2",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 657,
"aa_ref": "E",
"aa_start": 320,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3475,
"cdna_start": 1508,
"cds_end": null,
"cds_length": 1974,
"cds_start": 959,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000276054.9",
"gene_hgnc_id": 28855,
"gene_symbol": "ZNF630",
"hgvs_c": "c.959A>T",
"hgvs_p": "p.Glu320Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001282201.2",
"protein_coding": true,
"protein_id": "ENSP00000354683.4",
"strand": false,
"transcript": "ENST00000276054.9",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 657,
"aa_ref": "E",
"aa_start": 320,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2455,
"cdna_start": 1186,
"cds_end": null,
"cds_length": 1974,
"cds_start": 959,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000409324.7",
"gene_hgnc_id": 28855,
"gene_symbol": "ZNF630",
"hgvs_c": "c.959A>T",
"hgvs_p": "p.Glu320Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000386393.3",
"strand": false,
"transcript": "ENST00000409324.7",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 657,
"aa_ref": "E",
"aa_start": 320,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3178,
"cdna_start": 1211,
"cds_end": null,
"cds_length": 1974,
"cds_start": 959,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001037735.4",
"gene_hgnc_id": 28855,
"gene_symbol": "ZNF630",
"hgvs_c": "c.959A>T",
"hgvs_p": "p.Glu320Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001032824.2",
"strand": false,
"transcript": "NM_001037735.4",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 657,
"aa_ref": "E",
"aa_start": 320,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2750,
"cdna_start": 1484,
"cds_end": null,
"cds_length": 1974,
"cds_start": 959,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000871921.1",
"gene_hgnc_id": 28855,
"gene_symbol": "ZNF630",
"hgvs_c": "c.959A>T",
"hgvs_p": "p.Glu320Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541980.1",
"strand": false,
"transcript": "ENST00000871921.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 657,
"aa_ref": "E",
"aa_start": 320,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2441,
"cdna_start": 1174,
"cds_end": null,
"cds_length": 1974,
"cds_start": 959,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000951017.1",
"gene_hgnc_id": 28855,
"gene_symbol": "ZNF630",
"hgvs_c": "c.959A>T",
"hgvs_p": "p.Glu320Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621076.1",
"strand": false,
"transcript": "ENST00000951017.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 657,
"aa_ref": "E",
"aa_start": 320,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2634,
"cdna_start": 1338,
"cds_end": null,
"cds_length": 1974,
"cds_start": 959,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000951018.1",
"gene_hgnc_id": 28855,
"gene_symbol": "ZNF630",
"hgvs_c": "c.959A>T",
"hgvs_p": "p.Glu320Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621077.1",
"strand": false,
"transcript": "ENST00000951018.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 643,
"aa_ref": "E",
"aa_start": 306,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3234,
"cdna_start": 1267,
"cds_end": null,
"cds_length": 1932,
"cds_start": 917,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001190255.3",
"gene_hgnc_id": 28855,
"gene_symbol": "ZNF630",
"hgvs_c": "c.917A>T",
"hgvs_p": "p.Glu306Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001177184.1",
"strand": false,
"transcript": "NM_001190255.3",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 643,
"aa_ref": "E",
"aa_start": 306,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2220,
"cdna_start": 917,
"cds_end": null,
"cds_length": 1932,
"cds_start": 917,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000616492.4",
"gene_hgnc_id": 28855,
"gene_symbol": "ZNF630",
"hgvs_c": "c.917A>T",
"hgvs_p": "p.Glu306Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000480858.1",
"strand": false,
"transcript": "ENST00000616492.4",
"transcript_support_level": 5
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 533,
"aa_ref": "E",
"aa_start": 196,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2773,
"cdna_start": 1504,
"cds_end": null,
"cds_length": 1602,
"cds_start": 587,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001282202.3",
"gene_hgnc_id": 28855,
"gene_symbol": "ZNF630",
"hgvs_c": "c.587A>T",
"hgvs_p": "p.Glu196Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001269131.1",
"strand": false,
"transcript": "NM_001282202.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 80,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2791,
"cdna_start": null,
"cds_end": null,
"cds_length": 243,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000442455.8",
"gene_hgnc_id": 28855,
"gene_symbol": "ZNF630",
"hgvs_c": "c.*712A>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000393163.5",
"strand": false,
"transcript": "ENST00000442455.8",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1245,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 12,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000428463.5",
"gene_hgnc_id": 28855,
"gene_symbol": "ZNF630",
"hgvs_c": "n.238+967A>T",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000400030.1",
"strand": false,
"transcript": "ENST00000428463.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 397,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000614448.1",
"gene_hgnc_id": 41215,
"gene_symbol": "ZNF630-AS1",
"hgvs_c": "n.123+3051T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000614448.1",
"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": 1122,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_046742.2",
"gene_hgnc_id": 41215,
"gene_symbol": "ZNF630-AS1",
"hgvs_c": "n.123+3051T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_046742.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs782209898",
"effect": "missense_variant",
"frequency_reference_population": 0.000024864778,
"gene_hgnc_id": 28855,
"gene_symbol": "ZNF630",
"gnomad_exomes_ac": 18,
"gnomad_exomes_af": 0.0000164379,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 12,
"gnomad_genomes_af": 0.000107627,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 6,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.512,
"pos": 48059483,
"ref": "T",
"revel_prediction": "Benign",
"revel_score": 0.024,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001037735.4"
}
]
}