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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: 1-193180956-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=193180956&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"PM2",
"BP4"
],
"effects": [
"missense_variant"
],
"gene_symbol": "B3GALT2",
"hgnc_id": 917,
"hgvs_c": "c.607C>T",
"hgvs_p": "p.Arg203Cys",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 1,
"transcript": "NM_003783.3",
"verdict": "Uncertain_significance"
},
{
"benign_score": 9,
"criteria": [
"BP4",
"BS1",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "CDC73",
"hgnc_id": 16783,
"hgvs_c": "c.973-22839G>A",
"hgvs_p": null,
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -9,
"transcript": "NM_024529.5",
"verdict": "Benign"
},
{
"benign_score": 1,
"criteria": [
"PM2",
"BP4"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000308280",
"hgnc_id": null,
"hgvs_c": "n.144+29671C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 1,
"transcript": "ENST00000832983.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_score": 1,
"allele_count_reference_population": 36,
"alphamissense_prediction": "Uncertain_significance",
"alphamissense_score": 0.3666,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.35,
"chr": "1",
"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": 0.3631231486797333,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 422,
"aa_ref": "R",
"aa_start": 203,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3548,
"cdna_start": 1322,
"cds_end": null,
"cds_length": 1269,
"cds_start": 607,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_003783.3",
"gene_hgnc_id": 917,
"gene_symbol": "B3GALT2",
"hgvs_c": "c.607C>T",
"hgvs_p": "p.Arg203Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000367434.5",
"protein_coding": true,
"protein_id": "NP_003774.1",
"strand": false,
"transcript": "NM_003783.3",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 422,
"aa_ref": "R",
"aa_start": 203,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3548,
"cdna_start": 1322,
"cds_end": null,
"cds_length": 1269,
"cds_start": 607,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000367434.5",
"gene_hgnc_id": 917,
"gene_symbol": "B3GALT2",
"hgvs_c": "c.607C>T",
"hgvs_p": "p.Arg203Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_003783.3",
"protein_coding": true,
"protein_id": "ENSP00000356404.4",
"strand": false,
"transcript": "ENST00000367434.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 531,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5869,
"cdna_start": null,
"cds_end": null,
"cds_length": 1596,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_024529.5",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "c.973-22839G>A",
"hgvs_p": null,
"intron_rank": 10,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000367435.5",
"protein_coding": true,
"protein_id": "NP_078805.3",
"strand": true,
"transcript": "NM_024529.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 531,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5869,
"cdna_start": null,
"cds_end": null,
"cds_length": 1596,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000367435.5",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "c.973-22839G>A",
"hgvs_p": null,
"intron_rank": 10,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_024529.5",
"protein_coding": true,
"protein_id": "ENSP00000356405.4",
"strand": true,
"transcript": "ENST00000367435.5",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 422,
"aa_ref": "R",
"aa_start": 203,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2692,
"cdna_start": 808,
"cds_end": null,
"cds_length": 1269,
"cds_start": 607,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000958440.1",
"gene_hgnc_id": 917,
"gene_symbol": "B3GALT2",
"hgvs_c": "c.607C>T",
"hgvs_p": "p.Arg203Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000628499.1",
"strand": false,
"transcript": "ENST00000958440.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 531,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7295,
"cdna_start": null,
"cds_end": null,
"cds_length": 1596,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000958309.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "c.973-22839G>A",
"hgvs_p": null,
"intron_rank": 11,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000628368.1",
"strand": true,
"transcript": "ENST00000958309.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 530,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4952,
"cdna_start": null,
"cds_end": null,
"cds_length": 1593,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000958310.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "c.973-22842G>A",
"hgvs_p": null,
"intron_rank": 10,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000628369.1",
"strand": true,
"transcript": "ENST00000958310.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 498,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2462,
"cdna_start": null,
"cds_end": null,
"cds_length": 1497,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000864170.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "c.874-22839G>A",
"hgvs_p": null,
"intron_rank": 9,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534229.1",
"strand": true,
"transcript": "ENST00000864170.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 477,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2359,
"cdna_start": null,
"cds_end": null,
"cds_length": 1434,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000916534.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "c.973-22839G>A",
"hgvs_p": null,
"intron_rank": 10,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586593.1",
"strand": true,
"transcript": "ENST00000916534.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 450,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15275,
"cdna_start": null,
"cds_end": null,
"cds_length": 1353,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000635846.2",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "c.730-22839G>A",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000490035.1",
"strand": true,
"transcript": "ENST00000635846.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 429,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2222,
"cdna_start": null,
"cds_end": null,
"cds_length": 1290,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000864171.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "c.667-22839G>A",
"hgvs_p": null,
"intron_rank": 8,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534230.1",
"strand": true,
"transcript": "ENST00000864171.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 367,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3863,
"cdna_start": null,
"cds_end": null,
"cds_length": 1104,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 12,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000958311.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "c.481-22839G>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000628370.1",
"strand": true,
"transcript": "ENST00000958311.1",
"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": 4482,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000643006.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "n.1040+19766G>A",
"hgvs_p": null,
"intron_rank": 11,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000496633.1",
"strand": true,
"transcript": "ENST00000643006.1",
"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": 2102,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000648071.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "n.*949-22839G>A",
"hgvs_p": null,
"intron_rank": 11,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000497513.1",
"strand": true,
"transcript": "ENST00000648071.1",
"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": 2364,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000649895.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "n.1191-22839G>A",
"hgvs_p": null,
"intron_rank": 10,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000649895.1",
"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": 2212,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000650197.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "n.973-22839G>A",
"hgvs_p": null,
"intron_rank": 10,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000496929.1",
"strand": true,
"transcript": "ENST00000650197.1",
"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": 5870,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000713651.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "n.973-22839G>A",
"hgvs_p": null,
"intron_rank": 10,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000518953.1",
"strand": true,
"transcript": "ENST00000713651.1",
"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": 516,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000832983.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000308280",
"hgvs_c": "n.144+29671C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000832983.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1382754851",
"effect": "missense_variant",
"frequency_reference_population": 0.00002231523,
"gene_hgnc_id": 917,
"gene_symbol": "B3GALT2",
"gnomad_exomes_ac": 35,
"gnomad_exomes_af": 0.0000239536,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000657514,
"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": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.647,
"pos": 193180956,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.194,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_003783.3"
}
]
}