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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: 17-56847995-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=56847995&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "DGKE",
"hgnc_id": 2852,
"hgvs_c": "c.818G>A",
"hgvs_p": "p.Arg273Gln",
"inheritance_mode": "AR",
"pathogenic_score": 3,
"score": 3,
"transcript": "NM_003647.3",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "TRIM25",
"hgnc_id": 12932,
"hgvs_c": "n.*313+3948C>T",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "ENST00000648772.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP2",
"acmg_score": 3,
"allele_count_reference_population": 13,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.1968,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.37,
"chr": "17",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Inborn genetic diseases",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.44761931896209717,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 567,
"aa_ref": "R",
"aa_start": 273,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8608,
"cdna_start": 946,
"cds_end": null,
"cds_length": 1704,
"cds_start": 818,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_003647.3",
"gene_hgnc_id": 2852,
"gene_symbol": "DGKE",
"hgvs_c": "c.818G>A",
"hgvs_p": "p.Arg273Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000284061.8",
"protein_coding": true,
"protein_id": "NP_003638.1",
"strand": true,
"transcript": "NM_003647.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 567,
"aa_ref": "R",
"aa_start": 273,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8608,
"cdna_start": 946,
"cds_end": null,
"cds_length": 1704,
"cds_start": 818,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000284061.8",
"gene_hgnc_id": 2852,
"gene_symbol": "DGKE",
"hgvs_c": "c.818G>A",
"hgvs_p": "p.Arg273Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_003647.3",
"protein_coding": true,
"protein_id": "ENSP00000284061.3",
"strand": true,
"transcript": "ENST00000284061.8",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 455,
"aa_ref": "R",
"aa_start": 216,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5179,
"cdna_start": 648,
"cds_end": null,
"cds_length": 1368,
"cds_start": 647,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000572944.1",
"gene_hgnc_id": 2852,
"gene_symbol": "DGKE",
"hgvs_c": "c.647G>A",
"hgvs_p": "p.Arg216Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000458493.1",
"strand": true,
"transcript": "ENST00000572944.1",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 543,
"aa_ref": "R",
"aa_start": 273,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2372,
"cdna_start": 994,
"cds_end": null,
"cds_length": 1632,
"cds_start": 818,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000951727.1",
"gene_hgnc_id": 2852,
"gene_symbol": "DGKE",
"hgvs_c": "c.818G>A",
"hgvs_p": "p.Arg273Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621786.1",
"strand": true,
"transcript": "ENST00000951727.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 529,
"aa_ref": "R",
"aa_start": 273,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1852,
"cdna_start": 929,
"cds_end": null,
"cds_length": 1590,
"cds_start": 818,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000878325.1",
"gene_hgnc_id": 2852,
"gene_symbol": "DGKE",
"hgvs_c": "c.818G>A",
"hgvs_p": "p.Arg273Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548384.1",
"strand": true,
"transcript": "ENST00000878325.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 505,
"aa_ref": "R",
"aa_start": 273,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2189,
"cdna_start": 989,
"cds_end": null,
"cds_length": 1518,
"cds_start": 818,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000878324.1",
"gene_hgnc_id": 2852,
"gene_symbol": "DGKE",
"hgvs_c": "c.818G>A",
"hgvs_p": "p.Arg273Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548383.1",
"strand": true,
"transcript": "ENST00000878324.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 709,
"aa_ref": "R",
"aa_start": 291,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9225,
"cdna_start": 1191,
"cds_end": null,
"cds_length": 2130,
"cds_start": 872,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_047436959.1",
"gene_hgnc_id": 2852,
"gene_symbol": "DGKE",
"hgvs_c": "c.872G>A",
"hgvs_p": "p.Arg291Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047292915.1",
"strand": true,
"transcript": "XM_047436959.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 691,
"aa_ref": "R",
"aa_start": 273,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8980,
"cdna_start": 946,
"cds_end": null,
"cds_length": 2076,
"cds_start": 818,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_017025243.3",
"gene_hgnc_id": 2852,
"gene_symbol": "DGKE",
"hgvs_c": "c.818G>A",
"hgvs_p": "p.Arg273Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016880732.1",
"strand": true,
"transcript": "XM_017025243.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 585,
"aa_ref": "R",
"aa_start": 291,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8853,
"cdna_start": 1191,
"cds_end": null,
"cds_length": 1758,
"cds_start": 872,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_011525394.4",
"gene_hgnc_id": 2852,
"gene_symbol": "DGKE",
"hgvs_c": "c.872G>A",
"hgvs_p": "p.Arg291Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011523696.1",
"strand": true,
"transcript": "XM_011525394.4",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 561,
"aa_ref": "R",
"aa_start": 291,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8781,
"cdna_start": 1191,
"cds_end": null,
"cds_length": 1686,
"cds_start": 872,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_017025244.3",
"gene_hgnc_id": 2852,
"gene_symbol": "DGKE",
"hgvs_c": "c.872G>A",
"hgvs_p": "p.Arg291Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016880733.1",
"strand": true,
"transcript": "XM_017025244.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 543,
"aa_ref": "R",
"aa_start": 291,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2046,
"cdna_start": 1191,
"cds_end": null,
"cds_length": 1632,
"cds_start": 872,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_011525395.3",
"gene_hgnc_id": 2852,
"gene_symbol": "DGKE",
"hgvs_c": "c.872G>A",
"hgvs_p": "p.Arg291Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011523697.1",
"strand": true,
"transcript": "XM_011525395.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 539,
"aa_ref": "R",
"aa_start": 121,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8474,
"cdna_start": 440,
"cds_end": null,
"cds_length": 1620,
"cds_start": 362,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_047436960.1",
"gene_hgnc_id": 2852,
"gene_symbol": "DGKE",
"hgvs_c": "c.362G>A",
"hgvs_p": "p.Arg121Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047292916.1",
"strand": true,
"transcript": "XM_047436960.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 452,
"aa_ref": "R",
"aa_start": 291,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1781,
"cdna_start": 1191,
"cds_end": null,
"cds_length": 1359,
"cds_start": 872,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_011525396.3",
"gene_hgnc_id": 2852,
"gene_symbol": "DGKE",
"hgvs_c": "c.872G>A",
"hgvs_p": "p.Arg291Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011523698.1",
"strand": true,
"transcript": "XM_011525396.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1724,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XR_002958079.2",
"gene_hgnc_id": 2852,
"gene_symbol": "DGKE",
"hgvs_c": "n.1191G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_002958079.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4248,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 13,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000648772.1",
"gene_hgnc_id": 12932,
"gene_symbol": "TRIM25",
"hgvs_c": "n.*313+3948C>T",
"hgvs_p": null,
"intron_rank": 10,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000498158.1",
"strand": false,
"transcript": "ENST00000648772.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs312262695",
"effect": "missense_variant",
"frequency_reference_population": 0.000008074865,
"gene_hgnc_id": 2852,
"gene_symbol": "DGKE",
"gnomad_exomes_ac": 8,
"gnomad_exomes_af": 0.00000548703,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 5,
"gnomad_genomes_af": 0.0000329056,
"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": "Uncertain significance",
"phenotype_combined": "Inborn genetic diseases",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.679,
"pos": 56847995,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.23,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_003647.3"
}
]
}