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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: 15-44557613-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=44557613&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 44557613,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_003758.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF3J",
"gene_hgnc_id": 3270,
"hgvs_c": "c.534T>A",
"hgvs_p": "p.Ser178Arg",
"transcript": "NM_003758.4",
"protein_id": "NP_003749.2",
"transcript_support_level": null,
"aa_start": 178,
"aa_end": null,
"aa_length": 258,
"cds_start": 534,
"cds_end": null,
"cds_length": 777,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000261868.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003758.4"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF3J",
"gene_hgnc_id": 3270,
"hgvs_c": "c.534T>A",
"hgvs_p": "p.Ser178Arg",
"transcript": "ENST00000261868.10",
"protein_id": "ENSP00000261868.5",
"transcript_support_level": 1,
"aa_start": 178,
"aa_end": null,
"aa_length": 258,
"cds_start": 534,
"cds_end": null,
"cds_length": 777,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003758.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000261868.10"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF3J",
"gene_hgnc_id": 3270,
"hgvs_c": "c.387T>A",
"hgvs_p": "p.Ser129Arg",
"transcript": "NM_001284336.2",
"protein_id": "NP_001271265.1",
"transcript_support_level": null,
"aa_start": 129,
"aa_end": null,
"aa_length": 209,
"cds_start": 387,
"cds_end": null,
"cds_length": 630,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001284336.2"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF3J",
"gene_hgnc_id": 3270,
"hgvs_c": "c.387T>A",
"hgvs_p": "p.Ser129Arg",
"transcript": "ENST00000424492.7",
"protein_id": "ENSP00000414548.3",
"transcript_support_level": 4,
"aa_start": 129,
"aa_end": null,
"aa_length": 209,
"cds_start": 387,
"cds_end": null,
"cds_length": 630,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000424492.7"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF3J",
"gene_hgnc_id": 3270,
"hgvs_c": "c.168T>A",
"hgvs_p": "p.Ser56Arg",
"transcript": "ENST00000536248.1",
"protein_id": "ENSP00000443563.1",
"transcript_support_level": 2,
"aa_start": 56,
"aa_end": null,
"aa_length": 105,
"cds_start": 168,
"cds_end": null,
"cds_length": 318,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000536248.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": 39,
"intron_rank_end": null,
"gene_symbol": "SPG11",
"gene_hgnc_id": 11226,
"hgvs_c": "c.7152-2404A>T",
"hgvs_p": null,
"transcript": "ENST00000684235.1",
"protein_id": "ENSP00000508295.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2392,
"cds_start": null,
"cds_end": null,
"cds_length": 7179,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000684235.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "EIF3J",
"gene_hgnc_id": 3270,
"hgvs_c": "c.410-2636T>A",
"hgvs_p": null,
"transcript": "NM_001284335.2",
"protein_id": "NP_001271264.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 204,
"cds_start": null,
"cds_end": null,
"cds_length": 615,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001284335.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "EIF3J",
"gene_hgnc_id": 3270,
"hgvs_c": "c.410-2636T>A",
"hgvs_p": null,
"transcript": "ENST00000535391.5",
"protein_id": "ENSP00000440221.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 204,
"cds_start": null,
"cds_end": null,
"cds_length": 615,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000535391.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "EIF3J",
"gene_hgnc_id": 3270,
"hgvs_c": "c.263-2636T>A",
"hgvs_p": null,
"transcript": "ENST00000863133.1",
"protein_id": "ENSP00000533192.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 155,
"cds_start": null,
"cds_end": null,
"cds_length": 468,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000863133.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF3J",
"gene_hgnc_id": 3270,
"hgvs_c": "n.325T>A",
"hgvs_p": null,
"transcript": "ENST00000558053.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000558053.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EIF3J",
"gene_hgnc_id": 3270,
"hgvs_c": "n.108T>A",
"hgvs_p": null,
"transcript": "ENST00000558353.1",
"protein_id": "ENSP00000453282.1",
"transcript_support_level": 5,
"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": "ENST00000558353.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000259659",
"gene_hgnc_id": null,
"hgvs_c": "n.-216T>A",
"hgvs_p": null,
"transcript": "ENST00000558006.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000558006.1"
}
],
"gene_symbol": "EIF3J",
"gene_hgnc_id": 3270,
"dbsnp": null,
"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": 0.658758282661438,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.293,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9377,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.22,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.291,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_003758.4",
"gene_symbol": "EIF3J",
"hgnc_id": 3270,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.534T>A",
"hgvs_p": "p.Ser178Arg"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000684235.1",
"gene_symbol": "SPG11",
"hgnc_id": 11226,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.7152-2404A>T",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000558006.1",
"gene_symbol": "ENSG00000259659",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-216T>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}