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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: 1-225939828-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=225939828&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 225939828,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_003240.5",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LEFTY2",
"gene_hgnc_id": 3122,
"hgvs_c": "c.425A>G",
"hgvs_p": "p.Gln142Arg",
"transcript": "NM_003240.5",
"protein_id": "NP_003231.2",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 366,
"cds_start": 425,
"cds_end": null,
"cds_length": 1101,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000366820.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003240.5"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LEFTY2",
"gene_hgnc_id": 3122,
"hgvs_c": "c.425A>G",
"hgvs_p": "p.Gln142Arg",
"transcript": "ENST00000366820.10",
"protein_id": "ENSP00000355785.5",
"transcript_support_level": 1,
"aa_start": 142,
"aa_end": null,
"aa_length": 366,
"cds_start": 425,
"cds_end": null,
"cds_length": 1101,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003240.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000366820.10"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LEFTY2",
"gene_hgnc_id": 3122,
"hgvs_c": "c.323A>G",
"hgvs_p": "p.Gln108Arg",
"transcript": "NM_001172425.3",
"protein_id": "NP_001165896.1",
"transcript_support_level": null,
"aa_start": 108,
"aa_end": null,
"aa_length": 332,
"cds_start": 323,
"cds_end": null,
"cds_length": 999,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001172425.3"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LEFTY2",
"gene_hgnc_id": 3122,
"hgvs_c": "c.323A>G",
"hgvs_p": "p.Gln108Arg",
"transcript": "ENST00000420304.6",
"protein_id": "ENSP00000388009.2",
"transcript_support_level": 2,
"aa_start": 108,
"aa_end": null,
"aa_length": 332,
"cds_start": 323,
"cds_end": null,
"cds_length": 999,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000420304.6"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LEFTY2",
"gene_hgnc_id": 3122,
"hgvs_c": "c.425A>G",
"hgvs_p": "p.Gln142Arg",
"transcript": "XM_011544266.2",
"protein_id": "XP_011542568.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 260,
"cds_start": 425,
"cds_end": null,
"cds_length": 783,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011544266.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LEFTY2",
"gene_hgnc_id": 3122,
"hgvs_c": "n.274A>G",
"hgvs_p": null,
"transcript": "ENST00000474493.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000474493.1"
}
],
"gene_symbol": "LEFTY2",
"gene_hgnc_id": 3122,
"dbsnp": "rs429477",
"frequency_reference_population": 0.0015533725,
"hom_count_reference_population": 22,
"allele_count_reference_population": 2406,
"gnomad_exomes_af": 0.00146358,
"gnomad_genomes_af": 0.00237676,
"gnomad_exomes_ac": 2044,
"gnomad_genomes_ac": 362,
"gnomad_exomes_homalt": 20,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0047640204429626465,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.041,
"revel_prediction": "Benign",
"alphamissense_score": 0.0509,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.121,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_003240.5",
"gene_symbol": "LEFTY2",
"hgnc_id": 3122,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.425A>G",
"hgvs_p": "p.Gln142Arg"
}
],
"clinvar_disease": "LEFTY2-related disorder,Left-right axis malformations",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "Left-right axis malformations|LEFTY2-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}