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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: 20-59035053-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=59035053&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 59035053,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_016045.3",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRELID3B",
"gene_hgnc_id": 15892,
"hgvs_c": "c.539G>A",
"hgvs_p": "p.Gly180Glu",
"transcript": "NM_016045.3",
"protein_id": "NP_057129.2",
"transcript_support_level": null,
"aa_start": 180,
"aa_end": null,
"aa_length": 194,
"cds_start": 539,
"cds_end": null,
"cds_length": 585,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000355937.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_016045.3"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRELID3B",
"gene_hgnc_id": 15892,
"hgvs_c": "c.539G>A",
"hgvs_p": "p.Gly180Glu",
"transcript": "ENST00000355937.9",
"protein_id": "ENSP00000348206.4",
"transcript_support_level": 1,
"aa_start": 180,
"aa_end": null,
"aa_length": 194,
"cds_start": 539,
"cds_end": null,
"cds_length": 585,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_016045.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000355937.9"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRELID3B",
"gene_hgnc_id": 15892,
"hgvs_c": "c.509G>A",
"hgvs_p": "p.Gly170Glu",
"transcript": "ENST00000852164.1",
"protein_id": "ENSP00000522223.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 184,
"cds_start": 509,
"cds_end": null,
"cds_length": 555,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000852164.1"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRELID3B",
"gene_hgnc_id": 15892,
"hgvs_c": "c.449G>A",
"hgvs_p": "p.Gly150Glu",
"transcript": "NM_001256403.2",
"protein_id": "NP_001243332.1",
"transcript_support_level": null,
"aa_start": 150,
"aa_end": null,
"aa_length": 164,
"cds_start": 449,
"cds_end": null,
"cds_length": 495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001256403.2"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRELID3B",
"gene_hgnc_id": 15892,
"hgvs_c": "c.449G>A",
"hgvs_p": "p.Gly150Glu",
"transcript": "ENST00000371033.9",
"protein_id": "ENSP00000360072.5",
"transcript_support_level": 2,
"aa_start": 150,
"aa_end": null,
"aa_length": 164,
"cds_start": 449,
"cds_end": null,
"cds_length": 495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000371033.9"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRELID3B",
"gene_hgnc_id": 15892,
"hgvs_c": "c.419G>A",
"hgvs_p": "p.Gly140Glu",
"transcript": "ENST00000918587.1",
"protein_id": "ENSP00000588646.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 154,
"cds_start": 419,
"cds_end": null,
"cds_length": 465,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918587.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRELID3B",
"gene_hgnc_id": 15892,
"hgvs_c": "n.*351G>A",
"hgvs_p": null,
"transcript": "ENST00000463057.1",
"protein_id": "ENSP00000431440.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000463057.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLMO2-ATP5E",
"gene_hgnc_id": null,
"hgvs_c": "n.655G>A",
"hgvs_p": null,
"transcript": "NR_037929.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_037929.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLMO2-ATP5E",
"gene_hgnc_id": null,
"hgvs_c": "n.396G>A",
"hgvs_p": null,
"transcript": "NR_037930.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_037930.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRELID3B",
"gene_hgnc_id": 15892,
"hgvs_c": "n.*351G>A",
"hgvs_p": null,
"transcript": "ENST00000463057.1",
"protein_id": "ENSP00000431440.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000463057.1"
}
],
"gene_symbol": "PRELID3B",
"gene_hgnc_id": 15892,
"dbsnp": "rs781284187",
"frequency_reference_population": 0.0000055766504,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000410477,
"gnomad_genomes_af": 0.0000197163,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2135329246520996,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.112,
"revel_prediction": "Benign",
"alphamissense_score": 0.2114,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.28,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.906,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_016045.3",
"gene_symbol": "PRELID3B",
"hgnc_id": 15892,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.539G>A",
"hgvs_p": "p.Gly180Glu"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NR_037929.1",
"gene_symbol": "SLMO2-ATP5E",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.655G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}