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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: 4-1002387-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=1002387&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM5",
"PM2_Supporting",
"PP3_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "IDUA",
"hgnc_id": 5391,
"hgvs_c": "c.1091C>G",
"hgvs_p": "p.Thr364Arg",
"inheritance_mode": "AR",
"pathogenic_score": 5,
"score": 5,
"transcript": "NM_000203.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM5,PM2_Supporting,PP3_Moderate",
"acmg_score": 5,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.9392,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.42,
"chr": "4",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Mucopolysaccharidosis type 1",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "LP:1 US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9705232977867126,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 653,
"aa_ref": "T",
"aa_start": 364,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2174,
"cdna_start": 1132,
"cds_end": null,
"cds_length": 1962,
"cds_start": 1091,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_000203.5",
"gene_hgnc_id": 5391,
"gene_symbol": "IDUA",
"hgvs_c": "c.1091C>G",
"hgvs_p": "p.Thr364Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000514224.2",
"protein_coding": true,
"protein_id": "NP_000194.2",
"strand": true,
"transcript": "NM_000203.5",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 653,
"aa_ref": "T",
"aa_start": 364,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2174,
"cdna_start": 1132,
"cds_end": null,
"cds_length": 1962,
"cds_start": 1091,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000514224.2",
"gene_hgnc_id": 5391,
"gene_symbol": "IDUA",
"hgvs_c": "c.1091C>G",
"hgvs_p": "p.Thr364Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000203.5",
"protein_coding": true,
"protein_id": "ENSP00000425081.2",
"strand": true,
"transcript": "ENST00000514224.2",
"transcript_support_level": 2
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 653,
"aa_ref": "T",
"aa_start": 364,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2186,
"cdna_start": 1179,
"cds_end": null,
"cds_length": 1962,
"cds_start": 1091,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000247933.9",
"gene_hgnc_id": 5391,
"gene_symbol": "IDUA",
"hgvs_c": "c.1091C>G",
"hgvs_p": "p.Thr364Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000247933.4",
"strand": true,
"transcript": "ENST00000247933.9",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 678,
"aa_ref": "T",
"aa_start": 389,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2198,
"cdna_start": 1215,
"cds_end": null,
"cds_length": 2037,
"cds_start": 1166,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000962389.1",
"gene_hgnc_id": 5391,
"gene_symbol": "IDUA",
"hgvs_c": "c.1166C>G",
"hgvs_p": "p.Thr389Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000632448.1",
"strand": true,
"transcript": "ENST00000962389.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 666,
"aa_ref": "T",
"aa_start": 364,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2169,
"cdna_start": 1147,
"cds_end": null,
"cds_length": 2001,
"cds_start": 1091,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000871737.1",
"gene_hgnc_id": 5391,
"gene_symbol": "IDUA",
"hgvs_c": "c.1091C>G",
"hgvs_p": "p.Thr364Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541796.1",
"strand": true,
"transcript": "ENST00000871737.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 653,
"aa_ref": "T",
"aa_start": 364,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2729,
"cdna_start": 1110,
"cds_end": null,
"cds_length": 1962,
"cds_start": 1091,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000962388.1",
"gene_hgnc_id": 5391,
"gene_symbol": "IDUA",
"hgvs_c": "c.1091C>G",
"hgvs_p": "p.Thr364Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000632447.1",
"strand": true,
"transcript": "ENST00000962388.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 651,
"aa_ref": "T",
"aa_start": 364,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2128,
"cdna_start": 1152,
"cds_end": null,
"cds_length": 1956,
"cds_start": 1091,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000871736.1",
"gene_hgnc_id": 5391,
"gene_symbol": "IDUA",
"hgvs_c": "c.1091C>G",
"hgvs_p": "p.Thr364Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541795.1",
"strand": true,
"transcript": "ENST00000871736.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 642,
"aa_ref": "T",
"aa_start": 353,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2163,
"cdna_start": 1126,
"cds_end": null,
"cds_length": 1929,
"cds_start": 1058,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000871734.1",
"gene_hgnc_id": 5391,
"gene_symbol": "IDUA",
"hgvs_c": "c.1058C>G",
"hgvs_p": "p.Thr353Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541793.1",
"strand": true,
"transcript": "ENST00000871734.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 634,
"aa_ref": "T",
"aa_start": 332,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2072,
"cdna_start": 1051,
"cds_end": null,
"cds_length": 1905,
"cds_start": 995,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000871738.1",
"gene_hgnc_id": 5391,
"gene_symbol": "IDUA",
"hgvs_c": "c.995C>G",
"hgvs_p": "p.Thr332Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541797.1",
"strand": true,
"transcript": "ENST00000871738.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 617,
"aa_ref": "T",
"aa_start": 328,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2064,
"cdna_start": 1024,
"cds_end": null,
"cds_length": 1854,
"cds_start": 983,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000871735.1",
"gene_hgnc_id": 5391,
"gene_symbol": "IDUA",
"hgvs_c": "c.983C>G",
"hgvs_p": "p.Thr328Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541794.1",
"strand": true,
"transcript": "ENST00000871735.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 611,
"aa_ref": "T",
"aa_start": 364,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1985,
"cdna_start": 1129,
"cds_end": null,
"cds_length": 1836,
"cds_start": 1091,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000871739.1",
"gene_hgnc_id": 5391,
"gene_symbol": "IDUA",
"hgvs_c": "c.1091C>G",
"hgvs_p": "p.Thr364Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541798.1",
"strand": true,
"transcript": "ENST00000871739.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 570,
"aa_ref": "T",
"aa_start": 281,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1861,
"cdna_start": 878,
"cds_end": null,
"cds_length": 1713,
"cds_start": 842,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000962390.1",
"gene_hgnc_id": 5391,
"gene_symbol": "IDUA",
"hgvs_c": "c.842C>G",
"hgvs_p": "p.Thr281Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000632449.1",
"strand": true,
"transcript": "ENST00000962390.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 521,
"aa_ref": "T",
"aa_start": 232,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2182,
"cdna_start": 1147,
"cds_end": null,
"cds_length": 1566,
"cds_start": 695,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001363576.1",
"gene_hgnc_id": 5391,
"gene_symbol": "IDUA",
"hgvs_c": "c.695C>G",
"hgvs_p": "p.Thr232Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001350505.1",
"strand": true,
"transcript": "NM_001363576.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 632,
"aa_ref": "T",
"aa_start": 364,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2099,
"cdna_start": 1179,
"cds_end": null,
"cds_length": 1899,
"cds_start": 1091,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_047415650.1",
"gene_hgnc_id": 5391,
"gene_symbol": "IDUA",
"hgvs_c": "c.1091C>G",
"hgvs_p": "p.Thr364Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047271606.1",
"strand": true,
"transcript": "XM_047415650.1",
"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": 2185,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000514698.5",
"gene_hgnc_id": 5391,
"gene_symbol": "IDUA",
"hgvs_c": "n.1198C>G",
"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": "ENST00000514698.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2130,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000652070.1",
"gene_hgnc_id": 5391,
"gene_symbol": "IDUA",
"hgvs_c": "n.1147C>G",
"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": "ENST00000652070.1",
"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": 2218,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 14,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NR_110313.1",
"gene_hgnc_id": 5391,
"gene_symbol": "IDUA",
"hgvs_c": "n.1179C>G",
"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": "NR_110313.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs121965032",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 5391,
"gene_symbol": "IDUA",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"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": "Mucopolysaccharidosis type 1",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.787,
"pos": 1002387,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.901,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_000203.5"
}
]
}