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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: 19-41423039-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=41423039&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 41423039,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000709.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "c.1037G>A",
"hgvs_p": "p.Arg346His",
"transcript": "NM_000709.4",
"protein_id": "NP_000700.1",
"transcript_support_level": null,
"aa_start": 346,
"aa_end": null,
"aa_length": 445,
"cds_start": 1037,
"cds_end": null,
"cds_length": 1338,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000269980.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000709.4"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "c.1037G>A",
"hgvs_p": "p.Arg346His",
"transcript": "ENST00000269980.7",
"protein_id": "ENSP00000269980.2",
"transcript_support_level": 1,
"aa_start": 346,
"aa_end": null,
"aa_length": 445,
"cds_start": 1037,
"cds_end": null,
"cds_length": 1338,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000709.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000269980.7"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000255730",
"gene_hgnc_id": null,
"hgvs_c": "c.1139G>A",
"hgvs_p": "p.Arg380His",
"transcript": "ENST00000540732.3",
"protein_id": "ENSP00000443246.1",
"transcript_support_level": 2,
"aa_start": 380,
"aa_end": null,
"aa_length": 479,
"cds_start": 1139,
"cds_end": null,
"cds_length": 1440,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000540732.3"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "c.1265G>A",
"hgvs_p": "p.Arg422His",
"transcript": "ENST00000919033.1",
"protein_id": "ENSP00000589092.1",
"transcript_support_level": null,
"aa_start": 422,
"aa_end": null,
"aa_length": 521,
"cds_start": 1265,
"cds_end": null,
"cds_length": 1566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000919033.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "c.1112G>A",
"hgvs_p": "p.Arg371His",
"transcript": "ENST00000906426.1",
"protein_id": "ENSP00000576485.1",
"transcript_support_level": null,
"aa_start": 371,
"aa_end": null,
"aa_length": 470,
"cds_start": 1112,
"cds_end": null,
"cds_length": 1413,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906426.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "c.1109G>A",
"hgvs_p": "p.Arg370His",
"transcript": "ENST00000906427.1",
"protein_id": "ENSP00000576486.1",
"transcript_support_level": null,
"aa_start": 370,
"aa_end": null,
"aa_length": 469,
"cds_start": 1109,
"cds_end": null,
"cds_length": 1410,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906427.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "c.1076G>A",
"hgvs_p": "p.Arg359His",
"transcript": "ENST00000906422.1",
"protein_id": "ENSP00000576481.1",
"transcript_support_level": null,
"aa_start": 359,
"aa_end": null,
"aa_length": 458,
"cds_start": 1076,
"cds_end": null,
"cds_length": 1377,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906422.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "c.1046G>A",
"hgvs_p": "p.Arg349His",
"transcript": "ENST00000457836.6",
"protein_id": "ENSP00000416000.2",
"transcript_support_level": 2,
"aa_start": 349,
"aa_end": null,
"aa_length": 448,
"cds_start": 1046,
"cds_end": null,
"cds_length": 1347,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000457836.6"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "c.1034G>A",
"hgvs_p": "p.Arg345His",
"transcript": "NM_001164783.2",
"protein_id": "NP_001158255.1",
"transcript_support_level": null,
"aa_start": 345,
"aa_end": null,
"aa_length": 444,
"cds_start": 1034,
"cds_end": null,
"cds_length": 1335,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001164783.2"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "c.1034G>A",
"hgvs_p": "p.Arg345His",
"transcript": "ENST00000906421.1",
"protein_id": "ENSP00000576480.1",
"transcript_support_level": null,
"aa_start": 345,
"aa_end": null,
"aa_length": 444,
"cds_start": 1034,
"cds_end": null,
"cds_length": 1335,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906421.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "c.911G>A",
"hgvs_p": "p.Arg304His",
"transcript": "ENST00000967145.1",
"protein_id": "ENSP00000637204.1",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 403,
"cds_start": 911,
"cds_end": null,
"cds_length": 1212,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967145.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "c.875G>A",
"hgvs_p": "p.Arg292His",
"transcript": "ENST00000906424.1",
"protein_id": "ENSP00000576483.1",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 391,
"cds_start": 875,
"cds_end": null,
"cds_length": 1176,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906424.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "c.830G>A",
"hgvs_p": "p.Arg277His",
"transcript": "ENST00000906423.1",
"protein_id": "ENSP00000576482.1",
"transcript_support_level": null,
"aa_start": 277,
"aa_end": null,
"aa_length": 376,
"cds_start": 830,
"cds_end": null,
"cds_length": 1131,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906423.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "c.827G>A",
"hgvs_p": "p.Arg276His",
"transcript": "ENST00000967147.1",
"protein_id": "ENSP00000637206.1",
"transcript_support_level": null,
"aa_start": 276,
"aa_end": null,
"aa_length": 375,
"cds_start": 827,
"cds_end": null,
"cds_length": 1128,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967147.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"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.770G>A",
"hgvs_p": "p.Arg257His",
"transcript": "ENST00000906425.1",
"protein_id": "ENSP00000576484.1",
"transcript_support_level": null,
"aa_start": 257,
"aa_end": null,
"aa_length": 356,
"cds_start": 770,
"cds_end": null,
"cds_length": 1071,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906425.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "c.950G>A",
"hgvs_p": "p.Arg317His",
"transcript": "ENST00000542943.5",
"protein_id": "ENSP00000440345.1",
"transcript_support_level": 5,
"aa_start": 317,
"aa_end": null,
"aa_length": 327,
"cds_start": 950,
"cds_end": null,
"cds_length": 986,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000542943.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "c.407-1463G>A",
"hgvs_p": null,
"transcript": "ENST00000919034.1",
"protein_id": "ENSP00000589093.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 170,
"cds_start": null,
"cds_end": null,
"cds_length": 513,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000919034.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"hgvs_c": "c.-71G>A",
"hgvs_p": null,
"transcript": "ENST00000544905.1",
"protein_id": "ENSP00000445727.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 93,
"cds_start": null,
"cds_end": null,
"cds_length": 282,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000544905.1"
}
],
"gene_symbol": "BCKDHA",
"gene_hgnc_id": 986,
"dbsnp": "rs398123486",
"frequency_reference_population": 0.0000037355528,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000275092,
"gnomad_genomes_af": 0.0000131468,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9923007488250732,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.964,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9966,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.6,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.072,
"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": "NM_000709.4",
"gene_symbol": "BCKDHA",
"hgnc_id": 986,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1037G>A",
"hgvs_p": "p.Arg346His"
},
{
"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.1139G>A",
"hgvs_p": "p.Arg380His"
}
],
"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:1 LP:3",
"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
}