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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: 20-51784274-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=51784274&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 51784274,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_020436.5",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SALL4",
"gene_hgnc_id": 15924,
"hgvs_c": "c.3153G>A",
"hgvs_p": "p.Ala1051Ala",
"transcript": "NM_020436.5",
"protein_id": "NP_065169.1",
"transcript_support_level": null,
"aa_start": 1051,
"aa_end": null,
"aa_length": 1053,
"cds_start": 3153,
"cds_end": null,
"cds_length": 3162,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000217086.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_020436.5"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SALL4",
"gene_hgnc_id": 15924,
"hgvs_c": "c.3153G>A",
"hgvs_p": "p.Ala1051Ala",
"transcript": "ENST00000217086.9",
"protein_id": "ENSP00000217086.4",
"transcript_support_level": 1,
"aa_start": 1051,
"aa_end": null,
"aa_length": 1053,
"cds_start": 3153,
"cds_end": null,
"cds_length": 3162,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_020436.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000217086.9"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SALL4",
"gene_hgnc_id": 15924,
"hgvs_c": "c.1842G>A",
"hgvs_p": "p.Ala614Ala",
"transcript": "ENST00000395997.3",
"protein_id": "ENSP00000379319.3",
"transcript_support_level": 1,
"aa_start": 614,
"aa_end": null,
"aa_length": 616,
"cds_start": 1842,
"cds_end": null,
"cds_length": 1851,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000395997.3"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SALL4",
"gene_hgnc_id": 15924,
"hgvs_c": "c.822G>A",
"hgvs_p": "p.Ala274Ala",
"transcript": "ENST00000371539.7",
"protein_id": "ENSP00000360594.3",
"transcript_support_level": 1,
"aa_start": 274,
"aa_end": null,
"aa_length": 276,
"cds_start": 822,
"cds_end": null,
"cds_length": 831,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000371539.7"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SALL4",
"gene_hgnc_id": 15924,
"hgvs_c": "c.1842G>A",
"hgvs_p": "p.Ala614Ala",
"transcript": "NM_001318031.2",
"protein_id": "NP_001304960.1",
"transcript_support_level": null,
"aa_start": 614,
"aa_end": null,
"aa_length": 616,
"cds_start": 1842,
"cds_end": null,
"cds_length": 1851,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318031.2"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SALL4",
"gene_hgnc_id": 15924,
"hgvs_c": "c.2847G>A",
"hgvs_p": "p.Ala949Ala",
"transcript": "XM_047440318.1",
"protein_id": "XP_047296274.1",
"transcript_support_level": null,
"aa_start": 949,
"aa_end": null,
"aa_length": 951,
"cds_start": 2847,
"cds_end": null,
"cds_length": 2856,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047440318.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000303179",
"gene_hgnc_id": null,
"hgvs_c": "n.231-21C>T",
"hgvs_p": null,
"transcript": "ENST00000792520.1",
"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": "ENST00000792520.1"
}
],
"gene_symbol": "SALL4",
"gene_hgnc_id": 15924,
"dbsnp": "rs142551587",
"frequency_reference_population": 0.000106585496,
"hom_count_reference_population": 0,
"allele_count_reference_population": 172,
"gnomad_exomes_af": 0.000113573,
"gnomad_genomes_af": 0.0000394446,
"gnomad_exomes_ac": 166,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6299999952316284,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.63,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.29,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BP7,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_020436.5",
"gene_symbol": "SALL4",
"hgnc_id": 15924,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3153G>A",
"hgvs_p": "p.Ala1051Ala"
},
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000792520.1",
"gene_symbol": "ENSG00000303179",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.231-21C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Duane-radial ray syndrome,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "not provided|Duane-radial ray syndrome",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}