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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: 3-38550528-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=38550528&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 38550528,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000423572.7",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.5844C>T",
"hgvs_p": "p.Ile1948Ile",
"transcript": "NM_001099404.2",
"protein_id": "NP_001092874.1",
"transcript_support_level": null,
"aa_start": 1948,
"aa_end": null,
"aa_length": 2016,
"cds_start": 5844,
"cds_end": null,
"cds_length": 6051,
"cdna_start": 6053,
"cdna_end": null,
"cdna_length": 8519,
"mane_select": null,
"mane_plus": "ENST00000413689.6",
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.5844C>T",
"hgvs_p": "p.Ile1948Ile",
"transcript": "ENST00000413689.6",
"protein_id": "ENSP00000410257.1",
"transcript_support_level": 5,
"aa_start": 1948,
"aa_end": null,
"aa_length": 2016,
"cds_start": 5844,
"cds_end": null,
"cds_length": 6051,
"cdna_start": 6053,
"cdna_end": null,
"cdna_length": 8519,
"mane_select": null,
"mane_plus": "NM_001099404.2",
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.5841C>T",
"hgvs_p": "p.Ile1947Ile",
"transcript": "NM_000335.5",
"protein_id": "NP_000326.2",
"transcript_support_level": null,
"aa_start": 1947,
"aa_end": null,
"aa_length": 2015,
"cds_start": 5841,
"cds_end": null,
"cds_length": 6048,
"cdna_start": 6050,
"cdna_end": null,
"cdna_length": 8516,
"mane_select": "ENST00000423572.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.5841C>T",
"hgvs_p": "p.Ile1947Ile",
"transcript": "ENST00000423572.7",
"protein_id": "ENSP00000398266.2",
"transcript_support_level": 1,
"aa_start": 1947,
"aa_end": null,
"aa_length": 2015,
"cds_start": 5841,
"cds_end": null,
"cds_length": 6048,
"cdna_start": 6050,
"cdna_end": null,
"cdna_length": 8516,
"mane_select": "NM_000335.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.5844C>T",
"hgvs_p": "p.Ile1948Ile",
"transcript": "ENST00000333535.9",
"protein_id": "ENSP00000328968.4",
"transcript_support_level": 1,
"aa_start": 1948,
"aa_end": null,
"aa_length": 2016,
"cds_start": 5844,
"cds_end": null,
"cds_length": 6051,
"cdna_start": 6053,
"cdna_end": null,
"cdna_length": 8519,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.5841C>T",
"hgvs_p": "p.Ile1947Ile",
"transcript": "ENST00000327956.7",
"protein_id": "ENSP00000333674.7",
"transcript_support_level": 1,
"aa_start": 1947,
"aa_end": null,
"aa_length": 2015,
"cds_start": 5841,
"cds_end": null,
"cds_length": 6048,
"cdna_start": 5979,
"cdna_end": null,
"cdna_length": 8445,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.5790C>T",
"hgvs_p": "p.Ile1930Ile",
"transcript": "ENST00000414099.6",
"protein_id": "ENSP00000398962.2",
"transcript_support_level": 1,
"aa_start": 1930,
"aa_end": null,
"aa_length": 1998,
"cds_start": 5790,
"cds_end": null,
"cds_length": 5997,
"cdna_start": 5832,
"cdna_end": null,
"cdna_length": 8303,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.5745C>T",
"hgvs_p": "p.Ile1915Ile",
"transcript": "ENST00000455624.6",
"protein_id": "ENSP00000399524.2",
"transcript_support_level": 1,
"aa_start": 1915,
"aa_end": null,
"aa_length": 1983,
"cds_start": 5745,
"cds_end": null,
"cds_length": 5952,
"cdna_start": 5770,
"cdna_end": null,
"cdna_length": 7170,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.5682C>T",
"hgvs_p": "p.Ile1894Ile",
"transcript": "ENST00000450102.6",
"protein_id": "ENSP00000403355.2",
"transcript_support_level": 1,
"aa_start": 1894,
"aa_end": null,
"aa_length": 1962,
"cds_start": 5682,
"cds_end": null,
"cds_length": 5889,
"cdna_start": 5724,
"cdna_end": null,
"cdna_length": 6284,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.5844C>T",
"hgvs_p": "p.Ile1948Ile",
"transcript": "NM_198056.3",
"protein_id": "NP_932173.1",
"transcript_support_level": null,
"aa_start": 1948,
"aa_end": null,
"aa_length": 2016,
"cds_start": 5844,
"cds_end": null,
"cds_length": 6051,
"cdna_start": 6053,
"cdna_end": null,
"cdna_length": 8519,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.5790C>T",
"hgvs_p": "p.Ile1930Ile",
"transcript": "NM_001099405.2",
"protein_id": "NP_001092875.1",
"transcript_support_level": null,
"aa_start": 1930,
"aa_end": null,
"aa_length": 1998,
"cds_start": 5790,
"cds_end": null,
"cds_length": 5997,
"cdna_start": 5999,
"cdna_end": null,
"cdna_length": 8465,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.5787C>T",
"hgvs_p": "p.Ile1929Ile",
"transcript": "NM_001354701.2",
"protein_id": "NP_001341630.1",
"transcript_support_level": null,
"aa_start": 1929,
"aa_end": null,
"aa_length": 1997,
"cds_start": 5787,
"cds_end": null,
"cds_length": 5994,
"cdna_start": 5996,
"cdna_end": null,
"cdna_length": 8462,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.5745C>T",
"hgvs_p": "p.Ile1915Ile",
"transcript": "NM_001160160.2",
"protein_id": "NP_001153632.1",
"transcript_support_level": null,
"aa_start": 1915,
"aa_end": null,
"aa_length": 1983,
"cds_start": 5745,
"cds_end": null,
"cds_length": 5952,
"cdna_start": 5954,
"cdna_end": null,
"cdna_length": 8420,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.5682C>T",
"hgvs_p": "p.Ile1894Ile",
"transcript": "NM_001160161.2",
"protein_id": "NP_001153633.1",
"transcript_support_level": null,
"aa_start": 1894,
"aa_end": null,
"aa_length": 1962,
"cds_start": 5682,
"cds_end": null,
"cds_length": 5889,
"cdna_start": 5891,
"cdna_end": null,
"cdna_length": 8357,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.5682C>T",
"hgvs_p": "p.Ile1894Ile",
"transcript": "ENST00000449557.6",
"protein_id": "ENSP00000413996.2",
"transcript_support_level": 5,
"aa_start": 1894,
"aa_end": null,
"aa_length": 1962,
"cds_start": 5682,
"cds_end": null,
"cds_length": 5889,
"cdna_start": 5691,
"cdna_end": null,
"cdna_length": 5898,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.5841C>T",
"hgvs_p": "p.Ile1947Ile",
"transcript": "XM_011533991.3",
"protein_id": "XP_011532293.1",
"transcript_support_level": null,
"aa_start": 1947,
"aa_end": null,
"aa_length": 2015,
"cds_start": 5841,
"cds_end": null,
"cds_length": 6048,
"cdna_start": 6050,
"cdna_end": null,
"cdna_length": 8516,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "n.*5086C>T",
"hgvs_p": null,
"transcript": "ENST00000713730.1",
"protein_id": "ENSP00000519034.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8616,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "n.6590C>T",
"hgvs_p": null,
"transcript": "NR_176299.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9056,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "n.*5086C>T",
"hgvs_p": null,
"transcript": "ENST00000713730.1",
"protein_id": "ENSP00000519034.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8616,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"dbsnp": "rs13324293",
"frequency_reference_population": 0.012070375,
"hom_count_reference_population": 1890,
"allele_count_reference_population": 19465,
"gnomad_exomes_af": 0.00683002,
"gnomad_genomes_af": 0.0623145,
"gnomad_exomes_ac": 9974,
"gnomad_genomes_ac": 9491,
"gnomad_exomes_homalt": 863,
"gnomad_genomes_homalt": 1027,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.47999998927116394,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.48,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.819,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000423572.7",
"gene_symbol": "SCN5A",
"hgnc_id": 10593,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "SD,AD,AR",
"hgvs_c": "c.5841C>T",
"hgvs_p": "p.Ile1947Ile"
}
],
"clinvar_disease": " paroxysmal familial, type 1, type 1A,Brugada syndrome 1,Cardiac arrhythmia,Cardiomyopathy,Cardiovascular phenotype,Congenital long QT syndrome,Dilated cardiomyopathy 1E,Long QT syndrome 3,Primary dilated cardiomyopathy,Progressive familial heart block,Sick sinus syndrome 1,Ventricular fibrillation,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:15",
"phenotype_combined": "not specified|Cardiovascular phenotype|Dilated cardiomyopathy 1E|Ventricular fibrillation, paroxysmal familial, type 1|Sick sinus syndrome 1|Long QT syndrome 3|Progressive familial heart block, type 1A|Congenital long QT syndrome|Brugada syndrome 1|not provided|Primary dilated cardiomyopathy|Cardiomyopathy|Cardiac arrhythmia",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}