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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: 22-20859106-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=20859106&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"5_prime_UTR_variant"
],
"gene_symbol": "SNAP29",
"hgnc_id": 11133,
"hgvs_c": "c.-5G>A",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_004782.4",
"verdict": "Benign"
},
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "PI4KA",
"hgnc_id": 8983,
"hgvs_c": "c.-19+17C>T",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -20,
"transcript": "ENST00000449120.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_score": -20,
"allele_count_reference_population": 3087,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.65,
"chr": "22",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": "CEDNIK syndrome,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.6499999761581421,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 258,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4259,
"cdna_start": null,
"cds_end": null,
"cds_length": 777,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_004782.4",
"gene_hgnc_id": 11133,
"gene_symbol": "SNAP29",
"hgvs_c": "c.-5G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000215730.12",
"protein_coding": true,
"protein_id": "NP_004773.1",
"strand": true,
"transcript": "NM_004782.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 258,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4259,
"cdna_start": null,
"cds_end": null,
"cds_length": 777,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000215730.12",
"gene_hgnc_id": 11133,
"gene_symbol": "SNAP29",
"hgvs_c": "c.-5G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004782.4",
"protein_coding": true,
"protein_id": "ENSP00000215730.6",
"strand": true,
"transcript": "ENST00000215730.12",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 267,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1022,
"cdna_start": null,
"cds_end": null,
"cds_length": 804,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000880968.1",
"gene_hgnc_id": 11133,
"gene_symbol": "SNAP29",
"hgvs_c": "c.-5G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551027.1",
"strand": true,
"transcript": "ENST00000880968.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 258,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4443,
"cdna_start": null,
"cds_end": null,
"cds_length": 777,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000880966.1",
"gene_hgnc_id": 11133,
"gene_symbol": "SNAP29",
"hgvs_c": "c.-5G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551025.1",
"strand": true,
"transcript": "ENST00000880966.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 257,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1033,
"cdna_start": null,
"cds_end": null,
"cds_length": 774,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000938374.1",
"gene_hgnc_id": 11133,
"gene_symbol": "SNAP29",
"hgvs_c": "c.-5G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000608433.1",
"strand": true,
"transcript": "ENST00000938374.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 237,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 823,
"cdna_start": null,
"cds_end": null,
"cds_length": 714,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000880969.1",
"gene_hgnc_id": 11133,
"gene_symbol": "SNAP29",
"hgvs_c": "c.-5G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551028.1",
"strand": true,
"transcript": "ENST00000880969.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 225,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2437,
"cdna_start": null,
"cds_end": null,
"cds_length": 678,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000880967.1",
"gene_hgnc_id": 11133,
"gene_symbol": "SNAP29",
"hgvs_c": "c.-5G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551026.1",
"strand": true,
"transcript": "ENST00000880967.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 86,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 574,
"cdna_start": null,
"cds_end": null,
"cds_length": 261,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000449120.1",
"gene_hgnc_id": 8983,
"gene_symbol": "PI4KA",
"hgvs_c": "c.-19+17C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000402437.1",
"strand": false,
"transcript": "ENST00000449120.1",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 972,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000490458.1",
"gene_hgnc_id": 11133,
"gene_symbol": "SNAP29",
"hgvs_c": "n.26G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000490458.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs139884576",
"effect": "5_prime_UTR_variant",
"frequency_reference_population": 0.0019331834,
"gene_hgnc_id": 11133,
"gene_symbol": "SNAP29",
"gnomad_exomes_ac": 1521,
"gnomad_exomes_af": 0.00105294,
"gnomad_exomes_homalt": 26,
"gnomad_genomes_ac": 1566,
"gnomad_genomes_af": 0.0102813,
"gnomad_genomes_homalt": 22,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 48,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "CEDNIK syndrome|not provided|not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.047,
"pos": 20859106,
"ref": "G",
"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_004782.4"
}
]
}