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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: 2-166405843-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=166405843&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 166405843,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000643258.1",
"consequences": [
{
"aa_ref": "V",
"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": "SCN7A",
"gene_hgnc_id": 10594,
"hgvs_c": "c.4786G>C",
"hgvs_p": "p.Val1596Leu",
"transcript": "NM_002976.4",
"protein_id": "NP_002967.2",
"transcript_support_level": null,
"aa_start": 1596,
"aa_end": null,
"aa_length": 1682,
"cds_start": 4786,
"cds_end": null,
"cds_length": 5049,
"cdna_start": 5195,
"cdna_end": null,
"cdna_length": 7465,
"mane_select": "ENST00000643258.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": true,
"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": "SCN7A",
"gene_hgnc_id": 10594,
"hgvs_c": "c.4786G>C",
"hgvs_p": "p.Val1596Leu",
"transcript": "ENST00000643258.1",
"protein_id": "ENSP00000496114.1",
"transcript_support_level": null,
"aa_start": 1596,
"aa_end": null,
"aa_length": 1682,
"cds_start": 4786,
"cds_end": null,
"cds_length": 5049,
"cdna_start": 5195,
"cdna_end": null,
"cdna_length": 7465,
"mane_select": "NM_002976.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN7A",
"gene_hgnc_id": 10594,
"hgvs_c": "c.4786G>C",
"hgvs_p": "p.Val1596Leu",
"transcript": "ENST00000441411.2",
"protein_id": "ENSP00000403846.2",
"transcript_support_level": 1,
"aa_start": 1596,
"aa_end": null,
"aa_length": 1682,
"cds_start": 4786,
"cds_end": null,
"cds_length": 5049,
"cdna_start": 5065,
"cdna_end": null,
"cdna_length": 5965,
"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": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN7A",
"gene_hgnc_id": 10594,
"hgvs_c": "n.*2591G>C",
"hgvs_p": null,
"transcript": "ENST00000424326.5",
"protein_id": "ENSP00000396600.1",
"transcript_support_level": 1,
"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": 5337,
"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": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN7A",
"gene_hgnc_id": 10594,
"hgvs_c": "n.*2591G>C",
"hgvs_p": null,
"transcript": "ENST00000424326.5",
"protein_id": "ENSP00000396600.1",
"transcript_support_level": 1,
"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": 5337,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN7A",
"gene_hgnc_id": 10594,
"hgvs_c": "c.4786G>C",
"hgvs_p": "p.Val1596Leu",
"transcript": "XM_006712680.3",
"protein_id": "XP_006712743.1",
"transcript_support_level": null,
"aa_start": 1596,
"aa_end": null,
"aa_length": 1682,
"cds_start": 4786,
"cds_end": null,
"cds_length": 5049,
"cdna_start": 5082,
"cdna_end": null,
"cdna_length": 7352,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"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": "SCN7A",
"gene_hgnc_id": 10594,
"hgvs_c": "c.4786G>C",
"hgvs_p": "p.Val1596Leu",
"transcript": "XM_006712682.4",
"protein_id": "XP_006712745.1",
"transcript_support_level": null,
"aa_start": 1596,
"aa_end": null,
"aa_length": 1682,
"cds_start": 4786,
"cds_end": null,
"cds_length": 5049,
"cdna_start": 5320,
"cdna_end": null,
"cdna_length": 7590,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"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": "SCN7A",
"gene_hgnc_id": 10594,
"hgvs_c": "c.4786G>C",
"hgvs_p": "p.Val1596Leu",
"transcript": "XM_011511615.3",
"protein_id": "XP_011509917.1",
"transcript_support_level": null,
"aa_start": 1596,
"aa_end": null,
"aa_length": 1682,
"cds_start": 4786,
"cds_end": null,
"cds_length": 5049,
"cdna_start": 5266,
"cdna_end": null,
"cdna_length": 7536,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"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": "SCN7A",
"gene_hgnc_id": 10594,
"hgvs_c": "c.4786G>C",
"hgvs_p": "p.Val1596Leu",
"transcript": "XM_017004667.2",
"protein_id": "XP_016860156.1",
"transcript_support_level": null,
"aa_start": 1596,
"aa_end": null,
"aa_length": 1682,
"cds_start": 4786,
"cds_end": null,
"cds_length": 5049,
"cdna_start": 5239,
"cdna_end": null,
"cdna_length": 7509,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"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": "SCN7A",
"gene_hgnc_id": 10594,
"hgvs_c": "c.4786G>C",
"hgvs_p": "p.Val1596Leu",
"transcript": "XM_047445396.1",
"protein_id": "XP_047301352.1",
"transcript_support_level": null,
"aa_start": 1596,
"aa_end": null,
"aa_length": 1682,
"cds_start": 4786,
"cds_end": null,
"cds_length": 5049,
"cdna_start": 5455,
"cdna_end": null,
"cdna_length": 7725,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"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": "SCN7A",
"gene_hgnc_id": 10594,
"hgvs_c": "c.4786G>C",
"hgvs_p": "p.Val1596Leu",
"transcript": "XM_047445397.1",
"protein_id": "XP_047301353.1",
"transcript_support_level": null,
"aa_start": 1596,
"aa_end": null,
"aa_length": 1682,
"cds_start": 4786,
"cds_end": null,
"cds_length": 5049,
"cdna_start": 5374,
"cdna_end": null,
"cdna_length": 7644,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"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": "SCN7A",
"gene_hgnc_id": 10594,
"hgvs_c": "c.4786G>C",
"hgvs_p": "p.Val1596Leu",
"transcript": "XM_047445398.1",
"protein_id": "XP_047301354.1",
"transcript_support_level": null,
"aa_start": 1596,
"aa_end": null,
"aa_length": 1682,
"cds_start": 4786,
"cds_end": null,
"cds_length": 5049,
"cdna_start": 5330,
"cdna_end": null,
"cdna_length": 7600,
"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": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN7A",
"gene_hgnc_id": 10594,
"hgvs_c": "n.5010G>C",
"hgvs_p": null,
"transcript": "NR_045628.1",
"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": 7280,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SCN7A",
"gene_hgnc_id": 10594,
"dbsnp": "rs3791251",
"frequency_reference_population": 0.0960691,
"hom_count_reference_population": 8123,
"allele_count_reference_population": 154956,
"gnomad_exomes_af": 0.0976181,
"gnomad_genomes_af": 0.0811872,
"gnomad_exomes_ac": 142611,
"gnomad_genomes_ac": 12345,
"gnomad_exomes_homalt": 7526,
"gnomad_genomes_homalt": 597,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0017091929912567139,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.255,
"revel_prediction": "Benign",
"alphamissense_score": 0.0822,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.45,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.134,
"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,BA1",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000643258.1",
"gene_symbol": "SCN7A",
"hgnc_id": 10594,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.4786G>C",
"hgvs_p": "p.Val1596Leu"
}
],
"clinvar_disease": "SCN7A-related disorder",
"clinvar_classification": "Benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "SCN7A-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}