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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: 3-38550890-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=38550890&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"BP4"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SCN5A",
"hgnc_id": 10593,
"hgvs_c": "c.5482G>A",
"hgvs_p": "p.Ala1828Thr",
"inheritance_mode": "AD,AR,SD",
"pathogenic_score": 0,
"score": -1,
"transcript": "NM_198056.3",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4",
"acmg_score": -1,
"allele_count_reference_population": 67,
"alphamissense_prediction": null,
"alphamissense_score": 0.1979,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.09,
"chr": "3",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Cardiac arrhythmia,Cardiovascular phenotype,SCN5A-related disorder,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:5",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.0033426228910684586,
"computational_source_selected": "CardioboostCm",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 2016,
"aa_ref": "A",
"aa_start": 1828,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8519,
"cdna_start": 5691,
"cds_end": null,
"cds_length": 6051,
"cds_start": 5482,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "NM_001099404.2",
"gene_hgnc_id": 10593,
"gene_symbol": "SCN5A",
"hgvs_c": "c.5482G>A",
"hgvs_p": "p.Ala1828Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": "ENST00000413689.6",
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001092874.1",
"strand": false,
"transcript": "NM_001099404.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 2016,
"aa_ref": "A",
"aa_start": 1828,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8519,
"cdna_start": 5691,
"cds_end": null,
"cds_length": 6051,
"cds_start": 5482,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000413689.6",
"gene_hgnc_id": 10593,
"gene_symbol": "SCN5A",
"hgvs_c": "c.5482G>A",
"hgvs_p": "p.Ala1828Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": "NM_001099404.2",
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000410257.1",
"strand": false,
"transcript": "ENST00000413689.6",
"transcript_support_level": 5
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 2015,
"aa_ref": "A",
"aa_start": 1827,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8516,
"cdna_start": 5688,
"cds_end": null,
"cds_length": 6048,
"cds_start": 5479,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "NM_000335.5",
"gene_hgnc_id": 10593,
"gene_symbol": "SCN5A",
"hgvs_c": "c.5479G>A",
"hgvs_p": "p.Ala1827Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000423572.7",
"protein_coding": true,
"protein_id": "NP_000326.2",
"strand": false,
"transcript": "NM_000335.5",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 2015,
"aa_ref": "A",
"aa_start": 1827,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8516,
"cdna_start": 5688,
"cds_end": null,
"cds_length": 6048,
"cds_start": 5479,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000423572.7",
"gene_hgnc_id": 10593,
"gene_symbol": "SCN5A",
"hgvs_c": "c.5479G>A",
"hgvs_p": "p.Ala1827Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000335.5",
"protein_coding": true,
"protein_id": "ENSP00000398266.2",
"strand": false,
"transcript": "ENST00000423572.7",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 2016,
"aa_ref": "A",
"aa_start": 1828,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8519,
"cdna_start": 5691,
"cds_end": null,
"cds_length": 6051,
"cds_start": 5482,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000333535.9",
"gene_hgnc_id": 10593,
"gene_symbol": "SCN5A",
"hgvs_c": "c.5482G>A",
"hgvs_p": "p.Ala1828Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000328968.4",
"strand": false,
"transcript": "ENST00000333535.9",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 2015,
"aa_ref": "A",
"aa_start": 1827,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8445,
"cdna_start": 5617,
"cds_end": null,
"cds_length": 6048,
"cds_start": 5479,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000327956.7",
"gene_hgnc_id": 10593,
"gene_symbol": "SCN5A",
"hgvs_c": "c.5479G>A",
"hgvs_p": "p.Ala1827Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000333674.7",
"strand": false,
"transcript": "ENST00000327956.7",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1998,
"aa_ref": "A",
"aa_start": 1810,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8303,
"cdna_start": 5470,
"cds_end": null,
"cds_length": 5997,
"cds_start": 5428,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "ENST00000414099.6",
"gene_hgnc_id": 10593,
"gene_symbol": "SCN5A",
"hgvs_c": "c.5428G>A",
"hgvs_p": "p.Ala1810Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000398962.2",
"strand": false,
"transcript": "ENST00000414099.6",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1983,
"aa_ref": "A",
"aa_start": 1795,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7170,
"cdna_start": 5408,
"cds_end": null,
"cds_length": 5952,
"cds_start": 5383,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "ENST00000455624.6",
"gene_hgnc_id": 10593,
"gene_symbol": "SCN5A",
"hgvs_c": "c.5383G>A",
"hgvs_p": "p.Ala1795Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000399524.2",
"strand": false,
"transcript": "ENST00000455624.6",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1962,
"aa_ref": "A",
"aa_start": 1774,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6284,
"cdna_start": 5362,
"cds_end": null,
"cds_length": 5889,
"cds_start": 5320,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "ENST00000450102.6",
"gene_hgnc_id": 10593,
"gene_symbol": "SCN5A",
"hgvs_c": "c.5320G>A",
"hgvs_p": "p.Ala1774Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000403355.2",
"strand": false,
"transcript": "ENST00000450102.6",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 2016,
"aa_ref": "A",
"aa_start": 1828,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8519,
"cdna_start": 5691,
"cds_end": null,
"cds_length": 6051,
"cds_start": 5482,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "NM_198056.3",
"gene_hgnc_id": 10593,
"gene_symbol": "SCN5A",
"hgvs_c": "c.5482G>A",
"hgvs_p": "p.Ala1828Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_932173.1",
"strand": false,
"transcript": "NM_198056.3",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1998,
"aa_ref": "A",
"aa_start": 1810,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8465,
"cdna_start": 5637,
"cds_end": null,
"cds_length": 5997,
"cds_start": 5428,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "NM_001099405.2",
"gene_hgnc_id": 10593,
"gene_symbol": "SCN5A",
"hgvs_c": "c.5428G>A",
"hgvs_p": "p.Ala1810Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001092875.1",
"strand": false,
"transcript": "NM_001099405.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1997,
"aa_ref": "A",
"aa_start": 1809,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8462,
"cdna_start": 5634,
"cds_end": null,
"cds_length": 5994,
"cds_start": 5425,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "NM_001354701.2",
"gene_hgnc_id": 10593,
"gene_symbol": "SCN5A",
"hgvs_c": "c.5425G>A",
"hgvs_p": "p.Ala1809Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001341630.1",
"strand": false,
"transcript": "NM_001354701.2",
"transcript_support_level": null
},
{
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"aa_length": 1983,
"aa_ref": "A",
"aa_start": 1795,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8420,
"cdna_start": 5592,
"cds_end": null,
"cds_length": 5952,
"cds_start": 5383,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "NM_001160160.2",
"gene_hgnc_id": 10593,
"gene_symbol": "SCN5A",
"hgvs_c": "c.5383G>A",
"hgvs_p": "p.Ala1795Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001153632.1",
"strand": false,
"transcript": "NM_001160160.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1962,
"aa_ref": "A",
"aa_start": 1774,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8357,
"cdna_start": 5529,
"cds_end": null,
"cds_length": 5889,
"cds_start": 5320,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "NM_001160161.2",
"gene_hgnc_id": 10593,
"gene_symbol": "SCN5A",
"hgvs_c": "c.5320G>A",
"hgvs_p": "p.Ala1774Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001153633.1",
"strand": false,
"transcript": "NM_001160161.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1962,
"aa_ref": "A",
"aa_start": 1774,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5898,
"cdna_start": 5329,
"cds_end": null,
"cds_length": 5889,
"cds_start": 5320,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "ENST00000449557.6",
"gene_hgnc_id": 10593,
"gene_symbol": "SCN5A",
"hgvs_c": "c.5320G>A",
"hgvs_p": "p.Ala1774Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000413996.2",
"strand": false,
"transcript": "ENST00000449557.6",
"transcript_support_level": 5
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1918,
"aa_ref": "A",
"aa_start": 1730,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8215,
"cdna_start": 5388,
"cds_end": null,
"cds_length": 5757,
"cds_start": 5188,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "ENST00000970295.1",
"gene_hgnc_id": 10593,
"gene_symbol": "SCN5A",
"hgvs_c": "c.5188G>A",
"hgvs_p": "p.Ala1730Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000640354.1",
"strand": false,
"transcript": "ENST00000970295.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 2015,
"aa_ref": "A",
"aa_start": 1827,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8516,
"cdna_start": 5688,
"cds_end": null,
"cds_length": 6048,
"cds_start": 5479,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "XM_011533991.3",
"gene_hgnc_id": 10593,
"gene_symbol": "SCN5A",
"hgvs_c": "c.5479G>A",
"hgvs_p": "p.Ala1827Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011532293.1",
"strand": false,
"transcript": "XM_011533991.3",
"transcript_support_level": null
},
{
"aa_alt": null,
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"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 8616,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 29,
"exon_rank": 29,
"exon_rank_end": null,
"feature": "ENST00000713730.1",
"gene_hgnc_id": 10593,
"gene_symbol": "SCN5A",
"hgvs_c": "n.*4724G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000519034.1",
"strand": false,
"transcript": "ENST00000713730.1",
"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": 9056,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 28,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "NR_176299.1",
"gene_hgnc_id": 10593,
"gene_symbol": "SCN5A",
"hgvs_c": "n.6228G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_176299.1",
"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": 8616,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 29,
"exon_rank": 29,
"exon_rank_end": null,
"feature": "ENST00000713730.1",
"gene_hgnc_id": 10593,
"gene_symbol": "SCN5A",
"hgvs_c": "n.*4724G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000519034.1",
"strand": false,
"transcript": "ENST00000713730.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs774593360",
"effect": "missense_variant",
"frequency_reference_population": 0.00004152057,
"gene_hgnc_id": 10593,
"gene_symbol": "SCN5A",
"gnomad_exomes_ac": 61,
"gnomad_exomes_af": 0.0000417357,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 6,
"gnomad_genomes_af": 0.0000394534,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Cardiac arrhythmia|Cardiovascular phenotype|not provided|SCN5A-related disorder",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.695,
"pos": 38550890,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.682,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_198056.3"
}
]
}