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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: 3-38550362-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=38550362&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 38550362,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_198056.3",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.6010T>C",
"hgvs_p": "p.Phe2004Leu",
"transcript": "NM_001099404.2",
"protein_id": "NP_001092874.1",
"transcript_support_level": null,
"aa_start": 2004,
"aa_end": null,
"aa_length": 2016,
"cds_start": 6010,
"cds_end": null,
"cds_length": 6051,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": "ENST00000413689.6",
"biotype": "protein_coding",
"feature": "NM_001099404.2"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.6010T>C",
"hgvs_p": "p.Phe2004Leu",
"transcript": "ENST00000413689.6",
"protein_id": "ENSP00000410257.1",
"transcript_support_level": 5,
"aa_start": 2004,
"aa_end": null,
"aa_length": 2016,
"cds_start": 6010,
"cds_end": null,
"cds_length": 6051,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": "NM_001099404.2",
"biotype": "protein_coding",
"feature": "ENST00000413689.6"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.6007T>C",
"hgvs_p": "p.Phe2003Leu",
"transcript": "NM_000335.5",
"protein_id": "NP_000326.2",
"transcript_support_level": null,
"aa_start": 2003,
"aa_end": null,
"aa_length": 2015,
"cds_start": 6007,
"cds_end": null,
"cds_length": 6048,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000423572.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000335.5"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.6007T>C",
"hgvs_p": "p.Phe2003Leu",
"transcript": "ENST00000423572.7",
"protein_id": "ENSP00000398266.2",
"transcript_support_level": 1,
"aa_start": 2003,
"aa_end": null,
"aa_length": 2015,
"cds_start": 6007,
"cds_end": null,
"cds_length": 6048,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000335.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000423572.7"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.6010T>C",
"hgvs_p": "p.Phe2004Leu",
"transcript": "ENST00000333535.9",
"protein_id": "ENSP00000328968.4",
"transcript_support_level": 1,
"aa_start": 2004,
"aa_end": null,
"aa_length": 2016,
"cds_start": 6010,
"cds_end": null,
"cds_length": 6051,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000333535.9"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.6007T>C",
"hgvs_p": "p.Phe2003Leu",
"transcript": "ENST00000327956.7",
"protein_id": "ENSP00000333674.7",
"transcript_support_level": 1,
"aa_start": 2003,
"aa_end": null,
"aa_length": 2015,
"cds_start": 6007,
"cds_end": null,
"cds_length": 6048,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000327956.7"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.5956T>C",
"hgvs_p": "p.Phe1986Leu",
"transcript": "ENST00000414099.6",
"protein_id": "ENSP00000398962.2",
"transcript_support_level": 1,
"aa_start": 1986,
"aa_end": null,
"aa_length": 1998,
"cds_start": 5956,
"cds_end": null,
"cds_length": 5997,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000414099.6"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.5911T>C",
"hgvs_p": "p.Phe1971Leu",
"transcript": "ENST00000455624.6",
"protein_id": "ENSP00000399524.2",
"transcript_support_level": 1,
"aa_start": 1971,
"aa_end": null,
"aa_length": 1983,
"cds_start": 5911,
"cds_end": null,
"cds_length": 5952,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000455624.6"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.5848T>C",
"hgvs_p": "p.Phe1950Leu",
"transcript": "ENST00000450102.6",
"protein_id": "ENSP00000403355.2",
"transcript_support_level": 1,
"aa_start": 1950,
"aa_end": null,
"aa_length": 1962,
"cds_start": 5848,
"cds_end": null,
"cds_length": 5889,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000450102.6"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.6010T>C",
"hgvs_p": "p.Phe2004Leu",
"transcript": "NM_198056.3",
"protein_id": "NP_932173.1",
"transcript_support_level": null,
"aa_start": 2004,
"aa_end": null,
"aa_length": 2016,
"cds_start": 6010,
"cds_end": null,
"cds_length": 6051,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_198056.3"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.5956T>C",
"hgvs_p": "p.Phe1986Leu",
"transcript": "NM_001099405.2",
"protein_id": "NP_001092875.1",
"transcript_support_level": null,
"aa_start": 1986,
"aa_end": null,
"aa_length": 1998,
"cds_start": 5956,
"cds_end": null,
"cds_length": 5997,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001099405.2"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.5953T>C",
"hgvs_p": "p.Phe1985Leu",
"transcript": "NM_001354701.2",
"protein_id": "NP_001341630.1",
"transcript_support_level": null,
"aa_start": 1985,
"aa_end": null,
"aa_length": 1997,
"cds_start": 5953,
"cds_end": null,
"cds_length": 5994,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001354701.2"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.5911T>C",
"hgvs_p": "p.Phe1971Leu",
"transcript": "NM_001160160.2",
"protein_id": "NP_001153632.1",
"transcript_support_level": null,
"aa_start": 1971,
"aa_end": null,
"aa_length": 1983,
"cds_start": 5911,
"cds_end": null,
"cds_length": 5952,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001160160.2"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.5848T>C",
"hgvs_p": "p.Phe1950Leu",
"transcript": "NM_001160161.2",
"protein_id": "NP_001153633.1",
"transcript_support_level": null,
"aa_start": 1950,
"aa_end": null,
"aa_length": 1962,
"cds_start": 5848,
"cds_end": null,
"cds_length": 5889,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001160161.2"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.5848T>C",
"hgvs_p": "p.Phe1950Leu",
"transcript": "ENST00000449557.6",
"protein_id": "ENSP00000413996.2",
"transcript_support_level": 5,
"aa_start": 1950,
"aa_end": null,
"aa_length": 1962,
"cds_start": 5848,
"cds_end": null,
"cds_length": 5889,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000449557.6"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.5716T>C",
"hgvs_p": "p.Phe1906Leu",
"transcript": "ENST00000970295.1",
"protein_id": "ENSP00000640354.1",
"transcript_support_level": null,
"aa_start": 1906,
"aa_end": null,
"aa_length": 1918,
"cds_start": 5716,
"cds_end": null,
"cds_length": 5757,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970295.1"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.6007T>C",
"hgvs_p": "p.Phe2003Leu",
"transcript": "XM_011533991.3",
"protein_id": "XP_011532293.1",
"transcript_support_level": null,
"aa_start": 2003,
"aa_end": null,
"aa_length": 2015,
"cds_start": 6007,
"cds_end": null,
"cds_length": 6048,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533991.3"
},
{
"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.*5252T>C",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000713730.1"
},
{
"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.6756T>C",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_176299.1"
},
{
"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.*5252T>C",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000713730.1"
}
],
"gene_symbol": "SCN5A",
"gene_hgnc_id": 10593,
"dbsnp": "rs41311117",
"frequency_reference_population": 0.0035155262,
"hom_count_reference_population": 13,
"allele_count_reference_population": 5393,
"gnomad_exomes_af": 0.00365995,
"gnomad_genomes_af": 0.00216815,
"gnomad_exomes_ac": 5071,
"gnomad_genomes_ac": 322,
"gnomad_exomes_homalt": 13,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0051378607749938965,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.308,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2828,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.26,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.074,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_198056.3",
"gene_symbol": "SCN5A",
"hgnc_id": 10593,
"effects": [
"missense_variant"
],
"inheritance_mode": "SD,AD,AR",
"hgvs_c": "c.6010T>C",
"hgvs_p": "p.Phe2004Leu"
}
],
"clinvar_disease": " paroxysmal familial, type 1, type 1A,Brugada syndrome,Brugada syndrome 1,Cardiac arrhythmia,Cardiomyopathy,Cardiovascular phenotype,Dilated cardiomyopathy 1E,Long QT syndrome,Long QT syndrome 3,Progressive familial heart block,Sick sinus syndrome 1,Ventricular fibrillation,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:6 LB:13 B:4 O:1",
"phenotype_combined": "not specified|not provided|Long QT syndrome;Brugada syndrome|Brugada syndrome 1;Long QT syndrome 3|Cardiovascular phenotype|Brugada syndrome 1|Cardiomyopathy|Sick sinus syndrome 1|Dilated cardiomyopathy 1E|Progressive familial heart block, type 1A|Long QT syndrome 3|Ventricular fibrillation, paroxysmal familial, type 1|Cardiac arrhythmia",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}