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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: 3-38550984-C-CTCA (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=38550984&ref=C&alt=CTCA&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 38550984,
"ref": "C",
"alt": "CTCA",
"effect": "disruptive_inframe_insertion",
"transcript": "NM_198056.3",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "DE",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"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.5385_5387dupTGA",
"hgvs_p": "p.Tyr1795_Glu1796insAsp",
"transcript": "NM_001099404.2",
"protein_id": "NP_001092874.1",
"transcript_support_level": null,
"aa_start": 1796,
"aa_end": null,
"aa_length": 2016,
"cds_start": 5387,
"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": "E",
"aa_alt": "DE",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"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.5385_5387dupTGA",
"hgvs_p": "p.Tyr1795_Glu1796insAsp",
"transcript": "ENST00000413689.6",
"protein_id": "ENSP00000410257.1",
"transcript_support_level": 5,
"aa_start": 1796,
"aa_end": null,
"aa_length": 2016,
"cds_start": 5387,
"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": "E",
"aa_alt": "DE",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"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.5382_5384dupTGA",
"hgvs_p": "p.Tyr1794_Glu1795insAsp",
"transcript": "NM_000335.5",
"protein_id": "NP_000326.2",
"transcript_support_level": null,
"aa_start": 1795,
"aa_end": null,
"aa_length": 2015,
"cds_start": 5384,
"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": "E",
"aa_alt": "DE",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"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.5382_5384dupTGA",
"hgvs_p": "p.Tyr1794_Glu1795insAsp",
"transcript": "ENST00000423572.7",
"protein_id": "ENSP00000398266.2",
"transcript_support_level": 1,
"aa_start": 1795,
"aa_end": null,
"aa_length": 2015,
"cds_start": 5384,
"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": "E",
"aa_alt": "DE",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"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.5385_5387dupTGA",
"hgvs_p": "p.Tyr1795_Glu1796insAsp",
"transcript": "ENST00000333535.9",
"protein_id": "ENSP00000328968.4",
"transcript_support_level": 1,
"aa_start": 1796,
"aa_end": null,
"aa_length": 2016,
"cds_start": 5387,
"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": "E",
"aa_alt": "DE",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"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.5382_5384dupTGA",
"hgvs_p": "p.Tyr1794_Glu1795insAsp",
"transcript": "ENST00000327956.7",
"protein_id": "ENSP00000333674.7",
"transcript_support_level": 1,
"aa_start": 1795,
"aa_end": null,
"aa_length": 2015,
"cds_start": 5384,
"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": "E",
"aa_alt": "DE",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"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.5331_5333dupTGA",
"hgvs_p": "p.Tyr1777_Glu1778insAsp",
"transcript": "ENST00000414099.6",
"protein_id": "ENSP00000398962.2",
"transcript_support_level": 1,
"aa_start": 1778,
"aa_end": null,
"aa_length": 1998,
"cds_start": 5333,
"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": "E",
"aa_alt": "DE",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"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.5286_5288dupTGA",
"hgvs_p": "p.Tyr1762_Glu1763insAsp",
"transcript": "ENST00000455624.6",
"protein_id": "ENSP00000399524.2",
"transcript_support_level": 1,
"aa_start": 1763,
"aa_end": null,
"aa_length": 1983,
"cds_start": 5288,
"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": "E",
"aa_alt": "DE",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"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.5223_5225dupTGA",
"hgvs_p": "p.Tyr1741_Glu1742insAsp",
"transcript": "ENST00000450102.6",
"protein_id": "ENSP00000403355.2",
"transcript_support_level": 1,
"aa_start": 1742,
"aa_end": null,
"aa_length": 1962,
"cds_start": 5225,
"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": "E",
"aa_alt": "DE",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"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.5385_5387dupTGA",
"hgvs_p": "p.Tyr1795_Glu1796insAsp",
"transcript": "NM_198056.3",
"protein_id": "NP_932173.1",
"transcript_support_level": null,
"aa_start": 1796,
"aa_end": null,
"aa_length": 2016,
"cds_start": 5387,
"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": "E",
"aa_alt": "DE",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"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.5331_5333dupTGA",
"hgvs_p": "p.Tyr1777_Glu1778insAsp",
"transcript": "NM_001099405.2",
"protein_id": "NP_001092875.1",
"transcript_support_level": null,
"aa_start": 1778,
"aa_end": null,
"aa_length": 1998,
"cds_start": 5333,
"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": "E",
"aa_alt": "DE",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"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.5328_5330dupTGA",
"hgvs_p": "p.Tyr1776_Glu1777insAsp",
"transcript": "NM_001354701.2",
"protein_id": "NP_001341630.1",
"transcript_support_level": null,
"aa_start": 1777,
"aa_end": null,
"aa_length": 1997,
"cds_start": 5330,
"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": "E",
"aa_alt": "DE",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"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.5286_5288dupTGA",
"hgvs_p": "p.Tyr1762_Glu1763insAsp",
"transcript": "NM_001160160.2",
"protein_id": "NP_001153632.1",
"transcript_support_level": null,
"aa_start": 1763,
"aa_end": null,
"aa_length": 1983,
"cds_start": 5288,
"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": "E",
"aa_alt": "DE",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"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.5223_5225dupTGA",
"hgvs_p": "p.Tyr1741_Glu1742insAsp",
"transcript": "NM_001160161.2",
"protein_id": "NP_001153633.1",
"transcript_support_level": null,
"aa_start": 1742,
"aa_end": null,
"aa_length": 1962,
"cds_start": 5225,
"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": "E",
"aa_alt": "DE",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"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.5223_5225dupTGA",
"hgvs_p": "p.Tyr1741_Glu1742insAsp",
"transcript": "ENST00000449557.6",
"protein_id": "ENSP00000413996.2",
"transcript_support_level": 5,
"aa_start": 1742,
"aa_end": null,
"aa_length": 1962,
"cds_start": 5225,
"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": "E",
"aa_alt": "DE",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"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.5091_5093dupTGA",
"hgvs_p": "p.Tyr1697_Glu1698insAsp",
"transcript": "ENST00000970295.1",
"protein_id": "ENSP00000640354.1",
"transcript_support_level": null,
"aa_start": 1698,
"aa_end": null,
"aa_length": 1918,
"cds_start": 5093,
"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": "E",
"aa_alt": "DE",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_insertion"
],
"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.5382_5384dupTGA",
"hgvs_p": "p.Tyr1794_Glu1795insAsp",
"transcript": "XM_011533991.3",
"protein_id": "XP_011532293.1",
"transcript_support_level": null,
"aa_start": 1795,
"aa_end": null,
"aa_length": 2015,
"cds_start": 5384,
"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.*4627_*4629dupTGA",
"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.6131_6133dupTGA",
"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.*4627_*4629dupTGA",
"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": "rs397514449",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 8.006,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PM4_Supporting,PP3,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM1",
"PM2",
"PM4_Supporting",
"PP3",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_198056.3",
"gene_symbol": "SCN5A",
"hgnc_id": 10593,
"effects": [
"disruptive_inframe_insertion"
],
"inheritance_mode": "SD,AD,AR",
"hgvs_c": "c.5385_5387dupTGA",
"hgvs_p": "p.Tyr1795_Glu1796insAsp"
}
],
"clinvar_disease": "Brugada syndrome 1,Long QT syndrome 3,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Long QT syndrome 3|Brugada syndrome 1|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}