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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: 3-38846712-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=38846712&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 38846712,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_001349253.2",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.5358C>T",
"hgvs_p": "p.Gly1786Gly",
"transcript": "NM_001349253.2",
"protein_id": "NP_001336182.1",
"transcript_support_level": null,
"aa_start": 1786,
"aa_end": null,
"aa_length": 1791,
"cds_start": 5358,
"cds_end": null,
"cds_length": 5376,
"cdna_start": 5845,
"cdna_end": null,
"cdna_length": 6793,
"mane_select": "ENST00000302328.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.5358C>T",
"hgvs_p": "p.Gly1786Gly",
"transcript": "ENST00000302328.9",
"protein_id": "ENSP00000307599.3",
"transcript_support_level": 5,
"aa_start": 1786,
"aa_end": null,
"aa_length": 1791,
"cds_start": 5358,
"cds_end": null,
"cds_length": 5376,
"cdna_start": 5845,
"cdna_end": null,
"cdna_length": 6793,
"mane_select": "NM_001349253.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"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": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.5358C>T",
"hgvs_p": "p.Gly1786Gly",
"transcript": "NM_014139.3",
"protein_id": "NP_054858.2",
"transcript_support_level": null,
"aa_start": 1786,
"aa_end": null,
"aa_length": 1791,
"cds_start": 5358,
"cds_end": null,
"cds_length": 5376,
"cdna_start": 5557,
"cdna_end": null,
"cdna_length": 6505,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.5358C>T",
"hgvs_p": "p.Gly1786Gly",
"transcript": "ENST00000668754.1",
"protein_id": "ENSP00000499569.1",
"transcript_support_level": null,
"aa_start": 1786,
"aa_end": null,
"aa_length": 1791,
"cds_start": 5358,
"cds_end": null,
"cds_length": 5376,
"cdna_start": 6342,
"cdna_end": null,
"cdna_length": 7285,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.5244C>T",
"hgvs_p": "p.Gly1748Gly",
"transcript": "ENST00000456224.7",
"protein_id": "ENSP00000416757.3",
"transcript_support_level": 5,
"aa_start": 1748,
"aa_end": null,
"aa_length": 1753,
"cds_start": 5244,
"cds_end": null,
"cds_length": 5262,
"cdna_start": 5244,
"cdna_end": null,
"cdna_length": 5262,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.5178C>T",
"hgvs_p": "p.Gly1726Gly",
"transcript": "ENST00000675892.1",
"protein_id": "ENSP00000502318.1",
"transcript_support_level": null,
"aa_start": 1726,
"aa_end": null,
"aa_length": 1731,
"cds_start": 5178,
"cds_end": null,
"cds_length": 5196,
"cdna_start": 5178,
"cdna_end": null,
"cdna_length": 5196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.4977C>T",
"hgvs_p": "p.Gly1659Gly",
"transcript": "ENST00000676176.1",
"protein_id": "ENSP00000501891.1",
"transcript_support_level": null,
"aa_start": 1659,
"aa_end": null,
"aa_length": 1664,
"cds_start": 4977,
"cds_end": null,
"cds_length": 4995,
"cdna_start": 4977,
"cdna_end": null,
"cdna_length": 4995,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.5733C>T",
"hgvs_p": "p.Gly1911Gly",
"transcript": "XM_047447378.1",
"protein_id": "XP_047303334.1",
"transcript_support_level": null,
"aa_start": 1911,
"aa_end": null,
"aa_length": 1916,
"cds_start": 5733,
"cds_end": null,
"cds_length": 5751,
"cdna_start": 5959,
"cdna_end": null,
"cdna_length": 6907,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"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": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.5358C>T",
"hgvs_p": "p.Gly1786Gly",
"transcript": "XM_017005650.2",
"protein_id": "XP_016861139.1",
"transcript_support_level": null,
"aa_start": 1786,
"aa_end": null,
"aa_length": 1791,
"cds_start": 5358,
"cds_end": null,
"cds_length": 5376,
"cdna_start": 5726,
"cdna_end": null,
"cdna_length": 6674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"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": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.5085C>T",
"hgvs_p": "p.Gly1695Gly",
"transcript": "XM_017005651.2",
"protein_id": "XP_016861140.1",
"transcript_support_level": null,
"aa_start": 1695,
"aa_end": null,
"aa_length": 1700,
"cds_start": 5085,
"cds_end": null,
"cds_length": 5103,
"cdna_start": 5601,
"cdna_end": null,
"cdna_length": 6549,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.4695C>T",
"hgvs_p": "p.Gly1565Gly",
"transcript": "XM_011533321.3",
"protein_id": "XP_011531623.1",
"transcript_support_level": null,
"aa_start": 1565,
"aa_end": null,
"aa_length": 1570,
"cds_start": 4695,
"cds_end": null,
"cds_length": 4713,
"cdna_start": 4782,
"cdna_end": null,
"cdna_length": 5730,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.3762C>T",
"hgvs_p": "p.Gly1254Gly",
"transcript": "XM_017005653.2",
"protein_id": "XP_016861142.1",
"transcript_support_level": null,
"aa_start": 1254,
"aa_end": null,
"aa_length": 1259,
"cds_start": 3762,
"cds_end": null,
"cds_length": 3780,
"cdna_start": 4180,
"cdna_end": null,
"cdna_length": 5128,
"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": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "n.*1102C>T",
"hgvs_p": null,
"transcript": "ENST00000675223.1",
"protein_id": "ENSP00000502481.1",
"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": 5455,
"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": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "n.*2529C>T",
"hgvs_p": null,
"transcript": "ENST00000675672.1",
"protein_id": "ENSP00000502446.1",
"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": 5430,
"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": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "n.*5075C>T",
"hgvs_p": null,
"transcript": "ENST00000676045.1",
"protein_id": "ENSP00000501685.1",
"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": 5420,
"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": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "n.*1102C>T",
"hgvs_p": null,
"transcript": "ENST00000675223.1",
"protein_id": "ENSP00000502481.1",
"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": 5455,
"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": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "n.*2529C>T",
"hgvs_p": null,
"transcript": "ENST00000675672.1",
"protein_id": "ENSP00000502446.1",
"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": 5430,
"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": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "n.*5075C>T",
"hgvs_p": null,
"transcript": "ENST00000676045.1",
"protein_id": "ENSP00000501685.1",
"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": 5420,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"dbsnp": "rs1199517748",
"frequency_reference_population": 0.0000013682248,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136822,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.4699999988079071,
"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": -0.47,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.449,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 7,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_001349253.2",
"gene_symbol": "SCN11A",
"hgnc_id": 10583,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.5358C>T",
"hgvs_p": "p.Gly1786Gly"
}
],
"clinvar_disease": "Familial episodic pain syndrome with predominantly lower limb involvement,Hereditary sensory and autonomic neuropathy type 7",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Hereditary sensory and autonomic neuropathy type 7;Familial episodic pain syndrome with predominantly lower limb involvement",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}