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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: 19-41422754-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=41422754&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 41422754,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000269980.7",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "c.979G>A",
"hgvs_p": "p.Glu327Lys",
"transcript": "NM_000709.4",
"protein_id": "NP_000700.1",
"transcript_support_level": null,
"aa_start": 327,
"aa_end": null,
"aa_length": 445,
"cds_start": 979,
"cds_end": null,
"cds_length": 1338,
"cdna_start": 989,
"cdna_end": null,
"cdna_length": 1742,
"mane_select": "ENST00000269980.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "c.979G>A",
"hgvs_p": "p.Glu327Lys",
"transcript": "ENST00000269980.7",
"protein_id": "ENSP00000269980.2",
"transcript_support_level": 1,
"aa_start": 327,
"aa_end": null,
"aa_length": 445,
"cds_start": 979,
"cds_end": null,
"cds_length": 1338,
"cdna_start": 989,
"cdna_end": null,
"cdna_length": 1742,
"mane_select": "NM_000709.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000255730",
"gene_hgnc_id": null,
"hgvs_c": "c.1081G>A",
"hgvs_p": "p.Glu361Lys",
"transcript": "ENST00000540732.3",
"protein_id": "ENSP00000443246.1",
"transcript_support_level": 2,
"aa_start": 361,
"aa_end": null,
"aa_length": 479,
"cds_start": 1081,
"cds_end": null,
"cds_length": 1440,
"cdna_start": 1208,
"cdna_end": null,
"cdna_length": 1960,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "c.913G>A",
"hgvs_p": "p.Glu305Lys",
"transcript": "ENST00000457836.6",
"protein_id": "ENSP00000416000.2",
"transcript_support_level": 2,
"aa_start": 305,
"aa_end": null,
"aa_length": 448,
"cds_start": 913,
"cds_end": null,
"cds_length": 1347,
"cdna_start": 918,
"cdna_end": null,
"cdna_length": 1745,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "c.976G>A",
"hgvs_p": "p.Glu326Lys",
"transcript": "NM_001164783.2",
"protein_id": "NP_001158255.1",
"transcript_support_level": null,
"aa_start": 326,
"aa_end": null,
"aa_length": 444,
"cds_start": 976,
"cds_end": null,
"cds_length": 1335,
"cdna_start": 986,
"cdna_end": null,
"cdna_length": 1739,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "c.892G>A",
"hgvs_p": "p.Glu298Lys",
"transcript": "ENST00000542943.5",
"protein_id": "ENSP00000440345.1",
"transcript_support_level": 5,
"aa_start": 298,
"aa_end": null,
"aa_length": 327,
"cds_start": 892,
"cds_end": null,
"cds_length": 986,
"cdna_start": 900,
"cdna_end": null,
"cdna_length": 994,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "n.608G>A",
"hgvs_p": null,
"transcript": "ENST00000535632.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 615,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "n.*20G>A",
"hgvs_p": null,
"transcript": "ENST00000545787.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 587,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"dbsnp": "rs398123515",
"frequency_reference_population": 0.00004028824,
"hom_count_reference_population": 0,
"allele_count_reference_population": 65,
"gnomad_exomes_af": 0.0000437965,
"gnomad_genomes_af": 0.00000657592,
"gnomad_exomes_ac": 64,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9814372062683105,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.969,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9983,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.6,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.233,
"phylop100way_prediction": "Pathogenic",
"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": "PM2,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000269980.7",
"gene_symbol": "BCKDHA",
"hgnc_id": 986,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.979G>A",
"hgvs_p": "p.Glu327Lys"
},
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000540732.3",
"gene_symbol": "ENSG00000255730",
"hgnc_id": null,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1081G>A",
"hgvs_p": "p.Glu361Lys"
}
],
"clinvar_disease": "Maple syrup urine disease,Maple syrup urine disease type 1A,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:5 LP:1 US:1",
"phenotype_combined": "Maple syrup urine disease|not provided|Maple syrup urine disease type 1A",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}