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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: 3-38556474-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=38556474&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 38556474,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000423572.7",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.4404C>T",
"hgvs_p": "p.Val1468Val",
"transcript": "NM_001099404.2",
"protein_id": "NP_001092874.1",
"transcript_support_level": null,
"aa_start": 1468,
"aa_end": null,
"aa_length": 2016,
"cds_start": 4404,
"cds_end": null,
"cds_length": 6051,
"cdna_start": 4613,
"cdna_end": null,
"cdna_length": 8519,
"mane_select": null,
"mane_plus": "ENST00000413689.6",
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.4404C>T",
"hgvs_p": "p.Val1468Val",
"transcript": "ENST00000413689.6",
"protein_id": "ENSP00000410257.1",
"transcript_support_level": 5,
"aa_start": 1468,
"aa_end": null,
"aa_length": 2016,
"cds_start": 4404,
"cds_end": null,
"cds_length": 6051,
"cdna_start": 4613,
"cdna_end": null,
"cdna_length": 8519,
"mane_select": null,
"mane_plus": "NM_001099404.2",
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.4401C>T",
"hgvs_p": "p.Val1467Val",
"transcript": "NM_000335.5",
"protein_id": "NP_000326.2",
"transcript_support_level": null,
"aa_start": 1467,
"aa_end": null,
"aa_length": 2015,
"cds_start": 4401,
"cds_end": null,
"cds_length": 6048,
"cdna_start": 4610,
"cdna_end": null,
"cdna_length": 8516,
"mane_select": "ENST00000423572.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.4401C>T",
"hgvs_p": "p.Val1467Val",
"transcript": "ENST00000423572.7",
"protein_id": "ENSP00000398266.2",
"transcript_support_level": 1,
"aa_start": 1467,
"aa_end": null,
"aa_length": 2015,
"cds_start": 4401,
"cds_end": null,
"cds_length": 6048,
"cdna_start": 4610,
"cdna_end": null,
"cdna_length": 8516,
"mane_select": "NM_000335.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.4404C>T",
"hgvs_p": "p.Val1468Val",
"transcript": "ENST00000333535.9",
"protein_id": "ENSP00000328968.4",
"transcript_support_level": 1,
"aa_start": 1468,
"aa_end": null,
"aa_length": 2016,
"cds_start": 4404,
"cds_end": null,
"cds_length": 6051,
"cdna_start": 4613,
"cdna_end": null,
"cdna_length": 8519,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.4401C>T",
"hgvs_p": "p.Val1467Val",
"transcript": "ENST00000327956.7",
"protein_id": "ENSP00000333674.7",
"transcript_support_level": 1,
"aa_start": 1467,
"aa_end": null,
"aa_length": 2015,
"cds_start": 4401,
"cds_end": null,
"cds_length": 6048,
"cdna_start": 4539,
"cdna_end": null,
"cdna_length": 8445,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.4350C>T",
"hgvs_p": "p.Val1450Val",
"transcript": "ENST00000414099.6",
"protein_id": "ENSP00000398962.2",
"transcript_support_level": 1,
"aa_start": 1450,
"aa_end": null,
"aa_length": 1998,
"cds_start": 4350,
"cds_end": null,
"cds_length": 5997,
"cdna_start": 4392,
"cdna_end": null,
"cdna_length": 8303,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.4401C>T",
"hgvs_p": "p.Val1467Val",
"transcript": "ENST00000455624.6",
"protein_id": "ENSP00000399524.2",
"transcript_support_level": 1,
"aa_start": 1467,
"aa_end": null,
"aa_length": 1983,
"cds_start": 4401,
"cds_end": null,
"cds_length": 5952,
"cdna_start": 4426,
"cdna_end": null,
"cdna_length": 7170,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.4242C>T",
"hgvs_p": "p.Val1414Val",
"transcript": "ENST00000450102.6",
"protein_id": "ENSP00000403355.2",
"transcript_support_level": 1,
"aa_start": 1414,
"aa_end": null,
"aa_length": 1962,
"cds_start": 4242,
"cds_end": null,
"cds_length": 5889,
"cdna_start": 4284,
"cdna_end": null,
"cdna_length": 6284,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.4404C>T",
"hgvs_p": "p.Val1468Val",
"transcript": "NM_198056.3",
"protein_id": "NP_932173.1",
"transcript_support_level": null,
"aa_start": 1468,
"aa_end": null,
"aa_length": 2016,
"cds_start": 4404,
"cds_end": null,
"cds_length": 6051,
"cdna_start": 4613,
"cdna_end": null,
"cdna_length": 8519,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.4350C>T",
"hgvs_p": "p.Val1450Val",
"transcript": "NM_001099405.2",
"protein_id": "NP_001092875.1",
"transcript_support_level": null,
"aa_start": 1450,
"aa_end": null,
"aa_length": 1998,
"cds_start": 4350,
"cds_end": null,
"cds_length": 5997,
"cdna_start": 4559,
"cdna_end": null,
"cdna_length": 8465,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.4347C>T",
"hgvs_p": "p.Val1449Val",
"transcript": "NM_001354701.2",
"protein_id": "NP_001341630.1",
"transcript_support_level": null,
"aa_start": 1449,
"aa_end": null,
"aa_length": 1997,
"cds_start": 4347,
"cds_end": null,
"cds_length": 5994,
"cdna_start": 4556,
"cdna_end": null,
"cdna_length": 8462,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.4401C>T",
"hgvs_p": "p.Val1467Val",
"transcript": "NM_001160160.2",
"protein_id": "NP_001153632.1",
"transcript_support_level": null,
"aa_start": 1467,
"aa_end": null,
"aa_length": 1983,
"cds_start": 4401,
"cds_end": null,
"cds_length": 5952,
"cdna_start": 4610,
"cdna_end": null,
"cdna_length": 8420,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.4242C>T",
"hgvs_p": "p.Val1414Val",
"transcript": "NM_001160161.2",
"protein_id": "NP_001153633.1",
"transcript_support_level": null,
"aa_start": 1414,
"aa_end": null,
"aa_length": 1962,
"cds_start": 4242,
"cds_end": null,
"cds_length": 5889,
"cdna_start": 4451,
"cdna_end": null,
"cdna_length": 8357,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.4242C>T",
"hgvs_p": "p.Val1414Val",
"transcript": "ENST00000449557.6",
"protein_id": "ENSP00000413996.2",
"transcript_support_level": 5,
"aa_start": 1414,
"aa_end": null,
"aa_length": 1962,
"cds_start": 4242,
"cds_end": null,
"cds_length": 5889,
"cdna_start": 4251,
"cdna_end": null,
"cdna_length": 5898,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "c.4401C>T",
"hgvs_p": "p.Val1467Val",
"transcript": "XM_011533991.3",
"protein_id": "XP_011532293.1",
"transcript_support_level": null,
"aa_start": 1467,
"aa_end": null,
"aa_length": 2015,
"cds_start": 4401,
"cds_end": null,
"cds_length": 6048,
"cdna_start": 4610,
"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": 26,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "n.*3646C>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": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "n.5150C>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": 26,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"hgvs_c": "n.*3646C>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": "rs766197312",
"frequency_reference_population": 0.000024945182,
"hom_count_reference_population": 0,
"allele_count_reference_population": 40,
"gnomad_exomes_af": 0.0000220486,
"gnomad_genomes_af": 0.00005257,
"gnomad_exomes_ac": 32,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.36000001430511475,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.36,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.973,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -15,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BS1",
"acmg_by_gene": [
{
"score": -15,
"benign_score": 15,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000423572.7",
"gene_symbol": "SCN5A",
"hgnc_id": 10593,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "SD,AD,AR",
"hgvs_c": "c.4401C>T",
"hgvs_p": "p.Val1467Val"
}
],
"clinvar_disease": "Brugada syndrome,Cardiac arrhythmia,Cardiovascular phenotype,not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:5",
"phenotype_combined": "Cardiovascular phenotype|not provided|Brugada syndrome|Cardiac arrhythmia",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}