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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: 1-193233053-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=193233053&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 17,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "CDC73",
"hgnc_id": 16783,
"hgvs_c": "c.1215A>T",
"hgvs_p": "p.Ile405Ile",
"inheritance_mode": "AD",
"pathogenic_score": 2,
"score": -15,
"transcript": "NM_024529.5",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Very_Strong,BP7,BS2",
"acmg_score": -15,
"allele_count_reference_population": 5,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.56,
"chr": "1",
"clinvar_classification": "Likely benign",
"clinvar_disease": "Hereditary cancer-predisposing syndrome,Parathyroid carcinoma",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.5600000023841858,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 531,
"aa_ref": "I",
"aa_start": 405,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5869,
"cdna_start": 1385,
"cds_end": null,
"cds_length": 1596,
"cds_start": 1215,
"consequences": [
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "NM_024529.5",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "c.1215A>T",
"hgvs_p": "p.Ile405Ile",
"intron_rank": null,
"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": "I",
"aa_end": null,
"aa_length": 531,
"aa_ref": "I",
"aa_start": 405,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5869,
"cdna_start": 1385,
"cds_end": null,
"cds_length": 1596,
"cds_start": 1215,
"consequences": [
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000367435.5",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "c.1215A>T",
"hgvs_p": "p.Ile405Ile",
"intron_rank": null,
"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": "I",
"aa_end": null,
"aa_length": 531,
"aa_ref": "I",
"aa_start": 405,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7295,
"cdna_start": 1468,
"cds_end": null,
"cds_length": 1596,
"cds_start": 1215,
"consequences": [
"synonymous_variant"
],
"exon_count": 18,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000958309.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "c.1215A>T",
"hgvs_p": "p.Ile405Ile",
"intron_rank": null,
"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": "I",
"aa_end": null,
"aa_length": 530,
"aa_ref": "I",
"aa_start": 404,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4952,
"cdna_start": 1392,
"cds_end": null,
"cds_length": 1593,
"cds_start": 1212,
"consequences": [
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000958310.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "c.1212A>T",
"hgvs_p": "p.Ile404Ile",
"intron_rank": null,
"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": "I",
"aa_end": null,
"aa_length": 498,
"aa_ref": "I",
"aa_start": 372,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2462,
"cdna_start": 1355,
"cds_end": null,
"cds_length": 1497,
"cds_start": 1116,
"consequences": [
"synonymous_variant"
],
"exon_count": 16,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000864170.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "c.1116A>T",
"hgvs_p": "p.Ile372Ile",
"intron_rank": null,
"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": "I",
"aa_end": null,
"aa_length": 450,
"aa_ref": "I",
"aa_start": 324,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15275,
"cdna_start": 993,
"cds_end": null,
"cds_length": 1353,
"cds_start": 972,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000635846.2",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "c.972A>T",
"hgvs_p": "p.Ile324Ile",
"intron_rank": null,
"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": "I",
"aa_end": null,
"aa_length": 429,
"aa_ref": "I",
"aa_start": 303,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2222,
"cdna_start": 1135,
"cds_end": null,
"cds_length": 1290,
"cds_start": 909,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000864171.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "c.909A>T",
"hgvs_p": "p.Ile303Ile",
"intron_rank": null,
"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": "I",
"aa_end": null,
"aa_length": 367,
"aa_ref": "I",
"aa_start": 241,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3863,
"cdna_start": 808,
"cds_end": null,
"cds_length": 1104,
"cds_start": 723,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000958311.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "c.723A>T",
"hgvs_p": "p.Ile241Ile",
"intron_rank": null,
"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": 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.1155-3203A>T",
"hgvs_p": null,
"intron_rank": 13,
"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": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 764,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000477868.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "n.28A>T",
"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": "ENST00000477868.1",
"transcript_support_level": 3
},
{
"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": [
"non_coding_transcript_exon_variant"
],
"exon_count": 18,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000643006.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "n.*125A>T",
"hgvs_p": null,
"intron_rank": null,
"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": [
"non_coding_transcript_exon_variant"
],
"exon_count": 18,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000648071.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "n.*1191A>T",
"hgvs_p": null,
"intron_rank": null,
"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": 1325,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000649613.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "n.465A>T",
"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": "ENST00000649613.1",
"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": [
"non_coding_transcript_exon_variant"
],
"exon_count": 16,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000649895.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "n.1433A>T",
"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": "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": [
"non_coding_transcript_exon_variant"
],
"exon_count": 18,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000650197.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "n.1215A>T",
"hgvs_p": null,
"intron_rank": null,
"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": [
"non_coding_transcript_exon_variant"
],
"exon_count": 18,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000713651.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "n.1215A>T",
"hgvs_p": null,
"intron_rank": null,
"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": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4482,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 18,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000643006.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "n.*125A>T",
"hgvs_p": null,
"intron_rank": null,
"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": [
"3_prime_UTR_variant"
],
"exon_count": 18,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000648071.1",
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"hgvs_c": "n.*1191A>T",
"hgvs_p": null,
"intron_rank": null,
"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
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs765427308",
"effect": "synonymous_variant",
"frequency_reference_population": 0.000003421714,
"gene_hgnc_id": 16783,
"gene_symbol": "CDC73",
"gnomad_exomes_ac": 5,
"gnomad_exomes_af": 0.00000342171,
"gnomad_exomes_homalt": 0,
"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": "Likely benign",
"phenotype_combined": "Parathyroid carcinoma|Hereditary cancer-predisposing syndrome",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.58,
"pos": 193233053,
"ref": "A",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_024529.5"
}
]
}