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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: 3-46709165-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=46709165&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 46709165,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000643606.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMIE",
"gene_hgnc_id": 30800,
"hgvs_c": "c.251G>T",
"hgvs_p": "p.Arg84Leu",
"transcript": "NM_147196.3",
"protein_id": "NP_671729.2",
"transcript_support_level": null,
"aa_start": 84,
"aa_end": null,
"aa_length": 156,
"cds_start": 251,
"cds_end": null,
"cds_length": 471,
"cdna_start": 347,
"cdna_end": null,
"cdna_length": 1765,
"mane_select": "ENST00000643606.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMIE",
"gene_hgnc_id": 30800,
"hgvs_c": "c.251G>T",
"hgvs_p": "p.Arg84Leu",
"transcript": "ENST00000643606.3",
"protein_id": "ENSP00000494576.2",
"transcript_support_level": null,
"aa_start": 84,
"aa_end": null,
"aa_length": 156,
"cds_start": 251,
"cds_end": null,
"cds_length": 471,
"cdna_start": 347,
"cdna_end": null,
"cdna_length": 1765,
"mane_select": "NM_147196.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMIE",
"gene_hgnc_id": 30800,
"hgvs_c": "c.92G>T",
"hgvs_p": "p.Arg31Leu",
"transcript": "NM_001370524.1",
"protein_id": "NP_001357453.1",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 103,
"cds_start": 92,
"cds_end": null,
"cds_length": 312,
"cdna_start": 999,
"cdna_end": null,
"cdna_length": 2417,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMIE",
"gene_hgnc_id": 30800,
"hgvs_c": "c.92G>T",
"hgvs_p": "p.Arg31Leu",
"transcript": "NM_001370525.1",
"protein_id": "NP_001357454.1",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 103,
"cds_start": 92,
"cds_end": null,
"cds_length": 312,
"cdna_start": 689,
"cdna_end": null,
"cdna_length": 2107,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMIE",
"gene_hgnc_id": 30800,
"hgvs_c": "c.92G>T",
"hgvs_p": "p.Arg31Leu",
"transcript": "ENST00000644830.1",
"protein_id": "ENSP00000495111.1",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 103,
"cds_start": 92,
"cds_end": null,
"cds_length": 312,
"cdna_start": 249,
"cdna_end": null,
"cdna_length": 1634,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMIE",
"gene_hgnc_id": 30800,
"hgvs_c": "c.149G>T",
"hgvs_p": "p.Arg50Leu",
"transcript": "ENST00000651652.1",
"protein_id": "ENSP00000498953.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 92,
"cds_start": 149,
"cds_end": null,
"cds_length": 279,
"cdna_start": 149,
"cdna_end": null,
"cdna_length": 1038,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TMIE",
"gene_hgnc_id": 30800,
"dbsnp": "rs397517866",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8421752452850342,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.782,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9875,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.34,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.383,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.04,
"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": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Moderate,PP5_Moderate",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000643606.3",
"gene_symbol": "TMIE",
"hgnc_id": 30800,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.251G>T",
"hgvs_p": "p.Arg84Leu"
}
],
"clinvar_disease": "Rare genetic deafness",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Rare genetic deafness",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}