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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: 19-41424582-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=41424582&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "BCKDHA",
"hgnc_id": 986,
"hgvs_c": "c.1312T>A",
"hgvs_p": "p.Tyr438Asn",
"inheritance_mode": "AR",
"pathogenic_score": 18,
"score": 18,
"transcript": "NM_000709.4",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PS3",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ENSG00000255730",
"hgnc_id": null,
"hgvs_c": "c.1414T>A",
"hgvs_p": "p.Tyr472Asn",
"inheritance_mode": "",
"pathogenic_score": 18,
"score": 18,
"transcript": "ENST00000540732.3",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_score": 18,
"allele_count_reference_population": 92,
"alphamissense_prediction": null,
"alphamissense_score": 0.975,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.53,
"chr": "19",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": "Inborn genetic diseases,Maple syrup urine disease,Maple syrup urine disease type 1A,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:14 LP:2 O:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9806331396102905,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 445,
"aa_ref": "Y",
"aa_start": 438,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1742,
"cdna_start": 1322,
"cds_end": null,
"cds_length": 1338,
"cds_start": 1312,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_000709.4",
"gene_hgnc_id": 986,
"gene_symbol": "BCKDHA",
"hgvs_c": "c.1312T>A",
"hgvs_p": "p.Tyr438Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000269980.7",
"protein_coding": true,
"protein_id": "NP_000700.1",
"strand": true,
"transcript": "NM_000709.4",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 445,
"aa_ref": "Y",
"aa_start": 438,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1742,
"cdna_start": 1322,
"cds_end": null,
"cds_length": 1338,
"cds_start": 1312,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000269980.7",
"gene_hgnc_id": 986,
"gene_symbol": "BCKDHA",
"hgvs_c": "c.1312T>A",
"hgvs_p": "p.Tyr438Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000709.4",
"protein_coding": true,
"protein_id": "ENSP00000269980.2",
"strand": true,
"transcript": "ENST00000269980.7",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 479,
"aa_ref": "Y",
"aa_start": 472,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1960,
"cdna_start": 1541,
"cds_end": null,
"cds_length": 1440,
"cds_start": 1414,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000540732.3",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000255730",
"hgvs_c": "c.1414T>A",
"hgvs_p": "p.Tyr472Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000443246.1",
"strand": true,
"transcript": "ENST00000540732.3",
"transcript_support_level": 2
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 521,
"aa_ref": "Y",
"aa_start": 514,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1969,
"cdna_start": 1549,
"cds_end": null,
"cds_length": 1566,
"cds_start": 1540,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000919033.1",
"gene_hgnc_id": 986,
"gene_symbol": "BCKDHA",
"hgvs_c": "c.1540T>A",
"hgvs_p": "p.Tyr514Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000589092.1",
"strand": true,
"transcript": "ENST00000919033.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 470,
"aa_ref": "Y",
"aa_start": 463,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1816,
"cdna_start": 1397,
"cds_end": null,
"cds_length": 1413,
"cds_start": 1387,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000906426.1",
"gene_hgnc_id": 986,
"gene_symbol": "BCKDHA",
"hgvs_c": "c.1387T>A",
"hgvs_p": "p.Tyr463Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576485.1",
"strand": true,
"transcript": "ENST00000906426.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 469,
"aa_ref": "Y",
"aa_start": 462,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1813,
"cdna_start": 1394,
"cds_end": null,
"cds_length": 1410,
"cds_start": 1384,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000906427.1",
"gene_hgnc_id": 986,
"gene_symbol": "BCKDHA",
"hgvs_c": "c.1384T>A",
"hgvs_p": "p.Tyr462Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576486.1",
"strand": true,
"transcript": "ENST00000906427.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 458,
"aa_ref": "Y",
"aa_start": 451,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1800,
"cdna_start": 1377,
"cds_end": null,
"cds_length": 1377,
"cds_start": 1351,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000906422.1",
"gene_hgnc_id": 986,
"gene_symbol": "BCKDHA",
"hgvs_c": "c.1351T>A",
"hgvs_p": "p.Tyr451Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576481.1",
"strand": true,
"transcript": "ENST00000906422.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 448,
"aa_ref": "Y",
"aa_start": 441,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1745,
"cdna_start": 1326,
"cds_end": null,
"cds_length": 1347,
"cds_start": 1321,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000457836.6",
"gene_hgnc_id": 986,
"gene_symbol": "BCKDHA",
"hgvs_c": "c.1321T>A",
"hgvs_p": "p.Tyr441Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000416000.2",
"strand": true,
"transcript": "ENST00000457836.6",
"transcript_support_level": 2
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 444,
"aa_ref": "Y",
"aa_start": 437,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1739,
"cdna_start": 1319,
"cds_end": null,
"cds_length": 1335,
"cds_start": 1309,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001164783.2",
"gene_hgnc_id": 986,
"gene_symbol": "BCKDHA",
"hgvs_c": "c.1309T>A",
"hgvs_p": "p.Tyr437Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001158255.1",
"strand": true,
"transcript": "NM_001164783.2",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 444,
"aa_ref": "Y",
"aa_start": 437,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1767,
"cdna_start": 1344,
"cds_end": null,
"cds_length": 1335,
"cds_start": 1309,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000906421.1",
"gene_hgnc_id": 986,
"gene_symbol": "BCKDHA",
"hgvs_c": "c.1309T>A",
"hgvs_p": "p.Tyr437Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576480.1",
"strand": true,
"transcript": "ENST00000906421.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 403,
"aa_ref": "Y",
"aa_start": 396,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1620,
"cdna_start": 1203,
"cds_end": null,
"cds_length": 1212,
"cds_start": 1186,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000967145.1",
"gene_hgnc_id": 986,
"gene_symbol": "BCKDHA",
"hgvs_c": "c.1186T>A",
"hgvs_p": "p.Tyr396Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000637204.1",
"strand": true,
"transcript": "ENST00000967145.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 391,
"aa_ref": "Y",
"aa_start": 384,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1583,
"cdna_start": 1160,
"cds_end": null,
"cds_length": 1176,
"cds_start": 1150,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000906424.1",
"gene_hgnc_id": 986,
"gene_symbol": "BCKDHA",
"hgvs_c": "c.1150T>A",
"hgvs_p": "p.Tyr384Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576483.1",
"strand": true,
"transcript": "ENST00000906424.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 376,
"aa_ref": "Y",
"aa_start": 369,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1551,
"cdna_start": 1131,
"cds_end": null,
"cds_length": 1131,
"cds_start": 1105,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000906423.1",
"gene_hgnc_id": 986,
"gene_symbol": "BCKDHA",
"hgvs_c": "c.1105T>A",
"hgvs_p": "p.Tyr369Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576482.1",
"strand": true,
"transcript": "ENST00000906423.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 375,
"aa_ref": "Y",
"aa_start": 368,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1532,
"cdna_start": 1112,
"cds_end": null,
"cds_length": 1128,
"cds_start": 1102,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000967147.1",
"gene_hgnc_id": 986,
"gene_symbol": "BCKDHA",
"hgvs_c": "c.1102T>A",
"hgvs_p": "p.Tyr368Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000637206.1",
"strand": true,
"transcript": "ENST00000967147.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 356,
"aa_ref": "Y",
"aa_start": 349,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1475,
"cdna_start": 1055,
"cds_end": null,
"cds_length": 1071,
"cds_start": 1045,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000906425.1",
"gene_hgnc_id": 986,
"gene_symbol": "BCKDHA",
"hgvs_c": "c.1045T>A",
"hgvs_p": "p.Tyr349Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000576484.1",
"strand": true,
"transcript": "ENST00000906425.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 170,
"aa_ref": "Y",
"aa_start": 163,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 915,
"cdna_start": 497,
"cds_end": null,
"cds_length": 513,
"cds_start": 487,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000919034.1",
"gene_hgnc_id": 986,
"gene_symbol": "BCKDHA",
"hgvs_c": "c.487T>A",
"hgvs_p": "p.Tyr163Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000589093.1",
"strand": true,
"transcript": "ENST00000919034.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 93,
"aa_ref": "T",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 562,
"cdna_start": 142,
"cds_end": null,
"cds_length": 282,
"cds_start": 141,
"consequences": [
"synonymous_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000544905.1",
"gene_hgnc_id": 986,
"gene_symbol": "BCKDHA",
"hgvs_c": "c.141T>A",
"hgvs_p": "p.Thr47Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000445727.1",
"strand": true,
"transcript": "ENST00000544905.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs137852870",
"effect": "missense_variant",
"frequency_reference_population": 0.0000570789,
"gene_hgnc_id": 986,
"gene_symbol": "BCKDHA",
"gnomad_exomes_ac": 74,
"gnomad_exomes_af": 0.0000506971,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 18,
"gnomad_genomes_af": 0.000118301,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"phenotype_combined": "Maple syrup urine disease type 1A|not provided|Maple syrup urine disease|Inborn genetic diseases",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.587,
"pos": 41424582,
"ref": "T",
"revel_prediction": "Pathogenic",
"revel_score": 0.953,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000709.4"
}
]
}