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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: 11-123642501-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=123642501&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 123642501,
"ref": "C",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000299333.8",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3B",
"gene_hgnc_id": 20665,
"hgvs_c": "c.390G>T",
"hgvs_p": "p.Ala130Ala",
"transcript": "NM_001040151.2",
"protein_id": "NP_001035241.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 215,
"cds_start": 390,
"cds_end": null,
"cds_length": 648,
"cdna_start": 814,
"cdna_end": null,
"cdna_length": 5683,
"mane_select": "ENST00000299333.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3B",
"gene_hgnc_id": 20665,
"hgvs_c": "c.390G>T",
"hgvs_p": "p.Ala130Ala",
"transcript": "ENST00000299333.8",
"protein_id": "ENSP00000299333.3",
"transcript_support_level": 1,
"aa_start": 130,
"aa_end": null,
"aa_length": 215,
"cds_start": 390,
"cds_end": null,
"cds_length": 648,
"cdna_start": 814,
"cdna_end": null,
"cdna_length": 5683,
"mane_select": "NM_001040151.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3B",
"gene_hgnc_id": 20665,
"hgvs_c": "c.390G>T",
"hgvs_p": "p.Ala130Ala",
"transcript": "ENST00000392770.6",
"protein_id": "ENSP00000376523.2",
"transcript_support_level": 1,
"aa_start": 130,
"aa_end": null,
"aa_length": 215,
"cds_start": 390,
"cds_end": null,
"cds_length": 648,
"cdna_start": 1193,
"cdna_end": null,
"cdna_length": 6061,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3B",
"gene_hgnc_id": 20665,
"hgvs_c": "c.390G>T",
"hgvs_p": "p.Ala130Ala",
"transcript": "ENST00000530277.5",
"protein_id": "ENSP00000432785.1",
"transcript_support_level": 1,
"aa_start": 130,
"aa_end": null,
"aa_length": 215,
"cds_start": 390,
"cds_end": null,
"cds_length": 648,
"cdna_start": 797,
"cdna_end": null,
"cdna_length": 3984,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3B",
"gene_hgnc_id": 20665,
"hgvs_c": "c.390G>T",
"hgvs_p": "p.Ala130Ala",
"transcript": "NM_018400.4",
"protein_id": "NP_060870.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 215,
"cds_start": 390,
"cds_end": null,
"cds_length": 648,
"cdna_start": 1213,
"cdna_end": null,
"cdna_length": 6082,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3B",
"gene_hgnc_id": 20665,
"hgvs_c": "c.390G>T",
"hgvs_p": "p.Ala130Ala",
"transcript": "ENST00000657123.1",
"protein_id": "ENSP00000499439.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 215,
"cds_start": 390,
"cds_end": null,
"cds_length": 648,
"cdna_start": 552,
"cdna_end": null,
"cdna_length": 5408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3B",
"gene_hgnc_id": 20665,
"hgvs_c": "c.390G>T",
"hgvs_p": "p.Ala130Ala",
"transcript": "ENST00000657191.1",
"protein_id": "ENSP00000499755.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 215,
"cds_start": 390,
"cds_end": null,
"cds_length": 648,
"cdna_start": 532,
"cdna_end": null,
"cdna_length": 5388,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3B",
"gene_hgnc_id": 20665,
"hgvs_c": "c.390G>T",
"hgvs_p": "p.Ala130Ala",
"transcript": "XM_011542897.3",
"protein_id": "XP_011541199.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 215,
"cds_start": 390,
"cds_end": null,
"cds_length": 648,
"cdna_start": 814,
"cdna_end": null,
"cdna_length": 1357,
"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": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3B",
"gene_hgnc_id": 20665,
"hgvs_c": "n.84G>T",
"hgvs_p": null,
"transcript": "ENST00000659826.1",
"protein_id": "ENSP00000499518.1",
"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": 4570,
"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": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3B",
"gene_hgnc_id": 20665,
"hgvs_c": "n.390G>T",
"hgvs_p": null,
"transcript": "ENST00000667790.1",
"protein_id": "ENSP00000499234.1",
"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": 4703,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SCN3B",
"gene_hgnc_id": 20665,
"dbsnp": "rs148484744",
"frequency_reference_population": 0.00069571444,
"hom_count_reference_population": 9,
"allele_count_reference_population": 1123,
"gnomad_exomes_af": 0.000632057,
"gnomad_genomes_af": 0.00130685,
"gnomad_exomes_ac": 924,
"gnomad_genomes_ac": 199,
"gnomad_exomes_homalt": 7,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5199999809265137,
"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": -0.52,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.851,
"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": -17,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS2",
"acmg_by_gene": [
{
"score": -17,
"benign_score": 17,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000299333.8",
"gene_symbol": "SCN3B",
"hgnc_id": 20665,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.390G>T",
"hgvs_p": "p.Ala130Ala"
}
],
"clinvar_disease": "Brugada syndrome 7,Cardiovascular phenotype,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:2",
"phenotype_combined": "Cardiovascular phenotype|not specified|Brugada syndrome 7|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}