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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: 2-44942603-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=44942603&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 44942603,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000260653.5",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIX3",
"gene_hgnc_id": 10889,
"hgvs_c": "c.499G>T",
"hgvs_p": "p.Ala167Ser",
"transcript": "NM_005413.4",
"protein_id": "NP_005404.1",
"transcript_support_level": null,
"aa_start": 167,
"aa_end": null,
"aa_length": 332,
"cds_start": 499,
"cds_end": null,
"cds_length": 999,
"cdna_start": 902,
"cdna_end": null,
"cdna_length": 2713,
"mane_select": "ENST00000260653.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIX3",
"gene_hgnc_id": 10889,
"hgvs_c": "c.499G>T",
"hgvs_p": "p.Ala167Ser",
"transcript": "ENST00000260653.5",
"protein_id": "ENSP00000260653.3",
"transcript_support_level": 1,
"aa_start": 167,
"aa_end": null,
"aa_length": 332,
"cds_start": 499,
"cds_end": null,
"cds_length": 999,
"cdna_start": 902,
"cdna_end": null,
"cdna_length": 2713,
"mane_select": "NM_005413.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000225156",
"gene_hgnc_id": null,
"hgvs_c": "n.135+8227G>T",
"hgvs_p": null,
"transcript": "ENST00000760330.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 527,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SIX3-AS1",
"gene_hgnc_id": 40532,
"hgvs_c": "n.389-1770C>A",
"hgvs_p": null,
"transcript": "ENST00000760560.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1068,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SIX3-AS1",
"gene_hgnc_id": 40532,
"hgvs_c": "n.366-1770C>A",
"hgvs_p": null,
"transcript": "ENST00000760561.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 617,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SIX3",
"gene_hgnc_id": 10889,
"dbsnp": "rs387906868",
"frequency_reference_population": 0.0000112639955,
"hom_count_reference_population": 0,
"allele_count_reference_population": 18,
"gnomad_exomes_af": 0.00000968337,
"gnomad_genomes_af": 0.0000262753,
"gnomad_exomes_ac": 14,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9070274829864502,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.739,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.3575,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.21,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.497,
"phylop100way_prediction": "Uncertain_significance",
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000260653.5",
"gene_symbol": "SIX3",
"hgnc_id": 10889,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.499G>T",
"hgvs_p": "p.Ala167Ser"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000760330.1",
"gene_symbol": "ENSG00000225156",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.135+8227G>T",
"hgvs_p": null
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000760560.1",
"gene_symbol": "SIX3-AS1",
"hgnc_id": 40532,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.389-1770C>A",
"hgvs_p": null
}
],
"clinvar_disease": "Schizencephaly,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Schizencephaly|not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}