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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: 4-121882400-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=121882400&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "TRPC3",
"hgnc_id": 12335,
"hgvs_c": "c.2577T>C",
"hgvs_p": "p.Tyr859Tyr",
"inheritance_mode": "AD",
"pathogenic_score": 2,
"score": -4,
"transcript": "NM_001130698.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate",
"acmg_score": -4,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.54,
"chr": "4",
"clinvar_classification": "Likely benign",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.5400000214576721,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 921,
"aa_ref": "Y",
"aa_start": 859,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8401,
"cdna_start": 2957,
"cds_end": null,
"cds_length": 2766,
"cds_start": 2577,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_001130698.2",
"gene_hgnc_id": 12335,
"gene_symbol": "TRPC3",
"hgvs_c": "c.2577T>C",
"hgvs_p": "p.Tyr859Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000379645.8",
"protein_coding": true,
"protein_id": "NP_001124170.1",
"strand": false,
"transcript": "NM_001130698.2",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 921,
"aa_ref": "Y",
"aa_start": 859,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8401,
"cdna_start": 2957,
"cds_end": null,
"cds_length": 2766,
"cds_start": 2577,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000379645.8",
"gene_hgnc_id": 12335,
"gene_symbol": "TRPC3",
"hgvs_c": "c.2577T>C",
"hgvs_p": "p.Tyr859Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001130698.2",
"protein_coding": true,
"protein_id": "ENSP00000368966.3",
"strand": false,
"transcript": "ENST00000379645.8",
"transcript_support_level": 1
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 848,
"aa_ref": "Y",
"aa_start": 786,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3675,
"cdna_start": 2777,
"cds_end": null,
"cds_length": 2547,
"cds_start": 2358,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000264811.9",
"gene_hgnc_id": 12335,
"gene_symbol": "TRPC3",
"hgvs_c": "c.2358T>C",
"hgvs_p": "p.Tyr786Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000264811.5",
"strand": false,
"transcript": "ENST00000264811.9",
"transcript_support_level": 1
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 793,
"aa_ref": "Y",
"aa_start": 731,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2382,
"cdna_start": 2193,
"cds_end": null,
"cds_length": 2382,
"cds_start": 2193,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000513531.1",
"gene_hgnc_id": 12335,
"gene_symbol": "TRPC3",
"hgvs_c": "c.2193T>C",
"hgvs_p": "p.Tyr731Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000426899.1",
"strand": false,
"transcript": "ENST00000513531.1",
"transcript_support_level": 1
},
{
"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": 2700,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000506449.1",
"gene_hgnc_id": 12335,
"gene_symbol": "TRPC3",
"hgvs_c": "n.*1585T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000423866.1",
"strand": false,
"transcript": "ENST00000506449.1",
"transcript_support_level": 1
},
{
"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": 2700,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000506449.1",
"gene_hgnc_id": 12335,
"gene_symbol": "TRPC3",
"hgvs_c": "n.*1585T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000423866.1",
"strand": false,
"transcript": "ENST00000506449.1",
"transcript_support_level": 1
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 937,
"aa_ref": "Y",
"aa_start": 875,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3876,
"cdna_start": 2977,
"cds_end": null,
"cds_length": 2814,
"cds_start": 2625,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000949674.1",
"gene_hgnc_id": 12335,
"gene_symbol": "TRPC3",
"hgvs_c": "c.2625T>C",
"hgvs_p": "p.Tyr875Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619733.1",
"strand": false,
"transcript": "ENST00000949674.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 920,
"aa_ref": "Y",
"aa_start": 858,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4490,
"cdna_start": 2648,
"cds_end": null,
"cds_length": 2763,
"cds_start": 2574,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000871535.1",
"gene_hgnc_id": 12335,
"gene_symbol": "TRPC3",
"hgvs_c": "c.2574T>C",
"hgvs_p": "p.Tyr858Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541594.1",
"strand": false,
"transcript": "ENST00000871535.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 893,
"aa_ref": "Y",
"aa_start": 831,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8317,
"cdna_start": 2873,
"cds_end": null,
"cds_length": 2682,
"cds_start": 2493,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001366479.2",
"gene_hgnc_id": 12335,
"gene_symbol": "TRPC3",
"hgvs_c": "c.2493T>C",
"hgvs_p": "p.Tyr831Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001353408.1",
"strand": false,
"transcript": "NM_001366479.2",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 848,
"aa_ref": "Y",
"aa_start": 786,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3330,
"cdna_start": 2433,
"cds_end": null,
"cds_length": 2547,
"cds_start": 2358,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_003305.2",
"gene_hgnc_id": 12335,
"gene_symbol": "TRPC3",
"hgvs_c": "c.2358T>C",
"hgvs_p": "p.Tyr786Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_003296.1",
"strand": false,
"transcript": "NM_003305.2",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 937,
"aa_ref": "Y",
"aa_start": 875,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8449,
"cdna_start": 3005,
"cds_end": null,
"cds_length": 2814,
"cds_start": 2625,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "XM_011532217.4",
"gene_hgnc_id": 12335,
"gene_symbol": "TRPC3",
"hgvs_c": "c.2625T>C",
"hgvs_p": "p.Tyr875Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011530519.1",
"strand": false,
"transcript": "XM_011532217.4",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 936,
"aa_ref": "Y",
"aa_start": 874,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8446,
"cdna_start": 3002,
"cds_end": null,
"cds_length": 2811,
"cds_start": 2622,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "XM_017008578.3",
"gene_hgnc_id": 12335,
"gene_symbol": "TRPC3",
"hgvs_c": "c.2622T>C",
"hgvs_p": "p.Tyr874Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864067.1",
"strand": false,
"transcript": "XM_017008578.3",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 920,
"aa_ref": "Y",
"aa_start": 858,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8398,
"cdna_start": 2954,
"cds_end": null,
"cds_length": 2763,
"cds_start": 2574,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "XM_011532218.4",
"gene_hgnc_id": 12335,
"gene_symbol": "TRPC3",
"hgvs_c": "c.2574T>C",
"hgvs_p": "p.Tyr858Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011530520.1",
"strand": false,
"transcript": "XM_011532218.4",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1727973855",
"effect": "synonymous_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 12335,
"gene_symbol": "TRPC3",
"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": "Likely benign",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.331,
"pos": 121882400,
"ref": "A",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.029999999329447746,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.03,
"transcript": "NM_001130698.2"
}
]
}