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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: 14-74555629-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=74555629&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 74555629,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000261978.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LTBP2",
"gene_hgnc_id": 6715,
"hgvs_c": "c.895C>T",
"hgvs_p": "p.Arg299*",
"transcript": "NM_000428.3",
"protein_id": "NP_000419.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 1821,
"cds_start": 895,
"cds_end": null,
"cds_length": 5466,
"cdna_start": 1188,
"cdna_end": null,
"cdna_length": 8460,
"mane_select": "ENST00000261978.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LTBP2",
"gene_hgnc_id": 6715,
"hgvs_c": "c.895C>T",
"hgvs_p": "p.Arg299*",
"transcript": "ENST00000261978.9",
"protein_id": "ENSP00000261978.4",
"transcript_support_level": 1,
"aa_start": 299,
"aa_end": null,
"aa_length": 1821,
"cds_start": 895,
"cds_end": null,
"cds_length": 5466,
"cdna_start": 1188,
"cdna_end": null,
"cdna_length": 8460,
"mane_select": "NM_000428.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LTBP2",
"gene_hgnc_id": 6715,
"hgvs_c": "c.895C>T",
"hgvs_p": "p.Arg299*",
"transcript": "ENST00000556690.5",
"protein_id": "ENSP00000451477.1",
"transcript_support_level": 5,
"aa_start": 299,
"aa_end": null,
"aa_length": 1777,
"cds_start": 895,
"cds_end": null,
"cds_length": 5334,
"cdna_start": 1023,
"cdna_end": null,
"cdna_length": 5614,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LTBP2",
"gene_hgnc_id": 6715,
"hgvs_c": "n.895C>T",
"hgvs_p": null,
"transcript": "ENST00000553939.5",
"protein_id": "ENSP00000452110.1",
"transcript_support_level": 5,
"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": 6462,
"mane_select": null,
"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": "ENSG00000258425",
"gene_hgnc_id": null,
"hgvs_c": "n.233+3216G>A",
"hgvs_p": null,
"transcript": "ENST00000554552.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 518,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LTBP2",
"gene_hgnc_id": 6715,
"hgvs_c": "n.124-4279C>T",
"hgvs_p": null,
"transcript": "ENST00000557425.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 582,
"mane_select": null,
"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": "LOC124903346",
"gene_hgnc_id": null,
"hgvs_c": "n.99+3216G>A",
"hgvs_p": null,
"transcript": "XR_007064265.1",
"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": 1989,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LTBP2",
"gene_hgnc_id": 6715,
"dbsnp": "rs121918355",
"frequency_reference_population": 0.000010381959,
"hom_count_reference_population": 0,
"allele_count_reference_population": 15,
"gnomad_exomes_af": 0.000010382,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 15,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.550000011920929,
"computational_prediction_selected": "Pathogenic",
"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": 0.55,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.921,
"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": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PVS1",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000261978.9",
"gene_symbol": "LTBP2",
"hgnc_id": 6715,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR,AD,Unknown",
"hgvs_c": "c.895C>T",
"hgvs_p": "p.Arg299*"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000554552.1",
"gene_symbol": "ENSG00000258425",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.233+3216G>A",
"hgvs_p": null
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "XR_007064265.1",
"gene_symbol": "LOC124903346",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.99+3216G>A",
"hgvs_p": null
}
],
"clinvar_disease": " D, primary congenital, with ectopia lentis and with or without secondary glaucoma,Glaucoma 3,Microspherophakia,Microspherophakia and/or megalocornea,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3",
"phenotype_combined": "Glaucoma 3, primary congenital, D|Microspherophakia|not provided|Microspherophakia and/or megalocornea, with ectopia lentis and with or without secondary glaucoma",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}