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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: 19-35803070-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=35803070&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PRODH2",
"hgnc_id": 17325,
"hgvs_c": "c.1010G>A",
"hgvs_p": "p.Arg337His",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -2,
"transcript": "NM_021232.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_score": -2,
"allele_count_reference_population": 107,
"alphamissense_prediction": null,
"alphamissense_score": 0.0795,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.34,
"chr": "19",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.10063588619232178,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 460,
"aa_ref": "R",
"aa_start": 337,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1473,
"cdna_start": 1050,
"cds_end": null,
"cds_length": 1383,
"cds_start": 1010,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_021232.2",
"gene_hgnc_id": 17325,
"gene_symbol": "PRODH2",
"hgvs_c": "c.1010G>A",
"hgvs_p": "p.Arg337His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000653904.2",
"protein_coding": true,
"protein_id": "NP_067055.2",
"strand": false,
"transcript": "NM_021232.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 460,
"aa_ref": "R",
"aa_start": 337,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1473,
"cdna_start": 1050,
"cds_end": null,
"cds_length": 1383,
"cds_start": 1010,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000653904.2",
"gene_hgnc_id": 17325,
"gene_symbol": "PRODH2",
"hgvs_c": "c.1010G>A",
"hgvs_p": "p.Arg337His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_021232.2",
"protein_coding": true,
"protein_id": "ENSP00000499779.1",
"strand": false,
"transcript": "ENST00000653904.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 460,
"aa_ref": "R",
"aa_start": 337,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1677,
"cdna_start": 1256,
"cds_end": null,
"cds_length": 1383,
"cds_start": 1010,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000301175.7",
"gene_hgnc_id": 17325,
"gene_symbol": "PRODH2",
"hgvs_c": "c.1010G>A",
"hgvs_p": "p.Arg337His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000301175.4",
"strand": false,
"transcript": "ENST00000301175.7",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 499,
"aa_ref": "R",
"aa_start": 376,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1635,
"cdna_start": 1214,
"cds_end": null,
"cds_length": 1500,
"cds_start": 1127,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000881789.1",
"gene_hgnc_id": 17325,
"gene_symbol": "PRODH2",
"hgvs_c": "c.1127G>A",
"hgvs_p": "p.Arg376His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551848.1",
"strand": false,
"transcript": "ENST00000881789.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 459,
"aa_ref": "R",
"aa_start": 336,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1518,
"cdna_start": 1096,
"cds_end": null,
"cds_length": 1380,
"cds_start": 1007,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000881787.1",
"gene_hgnc_id": 17325,
"gene_symbol": "PRODH2",
"hgvs_c": "c.1007G>A",
"hgvs_p": "p.Arg336His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551846.1",
"strand": false,
"transcript": "ENST00000881787.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 458,
"aa_ref": "R",
"aa_start": 335,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1489,
"cdna_start": 1069,
"cds_end": null,
"cds_length": 1377,
"cds_start": 1004,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000881791.1",
"gene_hgnc_id": 17325,
"gene_symbol": "PRODH2",
"hgvs_c": "c.1004G>A",
"hgvs_p": "p.Arg335His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551850.1",
"strand": false,
"transcript": "ENST00000881791.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 408,
"aa_ref": "R",
"aa_start": 285,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1317,
"cdna_start": 894,
"cds_end": null,
"cds_length": 1227,
"cds_start": 854,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001378292.1",
"gene_hgnc_id": 17325,
"gene_symbol": "PRODH2",
"hgvs_c": "c.854G>A",
"hgvs_p": "p.Arg285His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001365221.1",
"strand": false,
"transcript": "NM_001378292.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 408,
"aa_ref": "R",
"aa_start": 285,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1378,
"cdna_start": 942,
"cds_end": null,
"cds_length": 1227,
"cds_start": 854,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000881785.1",
"gene_hgnc_id": 17325,
"gene_symbol": "PRODH2",
"hgvs_c": "c.854G>A",
"hgvs_p": "p.Arg285His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551844.1",
"strand": false,
"transcript": "ENST00000881785.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 407,
"aa_ref": "R",
"aa_start": 284,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1350,
"cdna_start": 929,
"cds_end": null,
"cds_length": 1224,
"cds_start": 851,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000881790.1",
"gene_hgnc_id": 17325,
"gene_symbol": "PRODH2",
"hgvs_c": "c.851G>A",
"hgvs_p": "p.Arg284His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551849.1",
"strand": false,
"transcript": "ENST00000881790.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 378,
"aa_ref": "R",
"aa_start": 337,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1387,
"cdna_start": 1050,
"cds_end": null,
"cds_length": 1137,
"cds_start": 1010,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001378293.1",
"gene_hgnc_id": 17325,
"gene_symbol": "PRODH2",
"hgvs_c": "c.1010G>A",
"hgvs_p": "p.Arg337His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001365222.1",
"strand": false,
"transcript": "NM_001378293.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 326,
"aa_ref": "R",
"aa_start": 285,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1231,
"cdna_start": 894,
"cds_end": null,
"cds_length": 981,
"cds_start": 854,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001378294.1",
"gene_hgnc_id": 17325,
"gene_symbol": "PRODH2",
"hgvs_c": "c.854G>A",
"hgvs_p": "p.Arg285His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001365223.1",
"strand": false,
"transcript": "NM_001378294.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 118,
"aa_ref": "R",
"aa_start": 77,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 567,
"cdna_start": 232,
"cds_end": null,
"cds_length": 357,
"cds_start": 230,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000588266.6",
"gene_hgnc_id": 17325,
"gene_symbol": "PRODH2",
"hgvs_c": "c.230G>A",
"hgvs_p": "p.Arg77His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000465214.2",
"strand": false,
"transcript": "ENST00000588266.6",
"transcript_support_level": 3
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 73,
"aa_ref": "R",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 612,
"cdna_start": 26,
"cds_end": null,
"cds_length": 222,
"cds_start": 26,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000589835.1",
"gene_hgnc_id": 17325,
"gene_symbol": "PRODH2",
"hgvs_c": "c.26G>A",
"hgvs_p": "p.Arg9His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000474199.1",
"strand": false,
"transcript": "ENST00000589835.1",
"transcript_support_level": 5
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 458,
"aa_ref": "R",
"aa_start": 335,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1479,
"cdna_start": 1044,
"cds_end": null,
"cds_length": 1377,
"cds_start": 1004,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000881792.1",
"gene_hgnc_id": 17325,
"gene_symbol": "PRODH2",
"hgvs_c": "c.1004G>A",
"hgvs_p": "p.Arg335His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551851.1",
"strand": false,
"transcript": "ENST00000881792.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 423,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1422,
"cdna_start": null,
"cds_end": null,
"cds_length": 1272,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000881786.1",
"gene_hgnc_id": 17325,
"gene_symbol": "PRODH2",
"hgvs_c": "c.1002-794G>A",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551845.1",
"strand": false,
"transcript": "ENST00000881786.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 422,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1405,
"cdna_start": null,
"cds_end": null,
"cds_length": 1269,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000881788.1",
"gene_hgnc_id": 17325,
"gene_symbol": "PRODH2",
"hgvs_c": "c.999-794G>A",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551847.1",
"strand": false,
"transcript": "ENST00000881788.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 371,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1167,
"cdna_start": null,
"cds_end": null,
"cds_length": 1116,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000881793.1",
"gene_hgnc_id": 17325,
"gene_symbol": "PRODH2",
"hgvs_c": "c.846-794G>A",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551852.1",
"strand": false,
"transcript": "ENST00000881793.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1956,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000587695.1",
"gene_hgnc_id": 17325,
"gene_symbol": "PRODH2",
"hgvs_c": "n.1535G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000587695.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs553353688",
"effect": "missense_variant",
"frequency_reference_population": 0.000069684145,
"gene_hgnc_id": 17325,
"gene_symbol": "PRODH2",
"gnomad_exomes_ac": 97,
"gnomad_exomes_af": 0.0000701237,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 10,
"gnomad_genomes_af": 0.0000656901,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.046,
"pos": 35803070,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.27,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_021232.2"
}
]
}