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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: 19-41386676-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=41386676&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 41386676,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_020158.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC5",
"gene_hgnc_id": 24662,
"hgvs_c": "c.665G>T",
"hgvs_p": "p.Arg222Leu",
"transcript": "NM_020158.4",
"protein_id": "NP_064543.3",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 235,
"cds_start": 665,
"cds_end": null,
"cds_length": 708,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000221233.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_020158.4"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC5",
"gene_hgnc_id": 24662,
"hgvs_c": "c.665G>T",
"hgvs_p": "p.Arg222Leu",
"transcript": "ENST00000221233.9",
"protein_id": "ENSP00000221233.3",
"transcript_support_level": 1,
"aa_start": 222,
"aa_end": null,
"aa_length": 235,
"cds_start": 665,
"cds_end": null,
"cds_length": 708,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_020158.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000221233.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000255730",
"gene_hgnc_id": null,
"hgvs_c": "c.210+8157C>A",
"hgvs_p": null,
"transcript": "ENST00000540732.3",
"protein_id": "ENSP00000443246.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 479,
"cds_start": null,
"cds_end": null,
"cds_length": 1440,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000540732.3"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC5",
"gene_hgnc_id": 24662,
"hgvs_c": "c.731G>T",
"hgvs_p": "p.Arg244Leu",
"transcript": "ENST00000593771.2",
"protein_id": "ENSP00000471557.2",
"transcript_support_level": 3,
"aa_start": 244,
"aa_end": null,
"aa_length": 257,
"cds_start": 731,
"cds_end": null,
"cds_length": 774,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000593771.2"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC5",
"gene_hgnc_id": 24662,
"hgvs_c": "c.662G>T",
"hgvs_p": "p.Arg221Leu",
"transcript": "ENST00000916935.1",
"protein_id": "ENSP00000586994.1",
"transcript_support_level": null,
"aa_start": 221,
"aa_end": null,
"aa_length": 234,
"cds_start": 662,
"cds_end": null,
"cds_length": 705,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916935.1"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC5",
"gene_hgnc_id": 24662,
"hgvs_c": "c.659G>T",
"hgvs_p": "p.Arg220Leu",
"transcript": "ENST00000916937.1",
"protein_id": "ENSP00000586996.1",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 233,
"cds_start": 659,
"cds_end": null,
"cds_length": 702,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916937.1"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC5",
"gene_hgnc_id": 24662,
"hgvs_c": "c.644G>T",
"hgvs_p": "p.Arg215Leu",
"transcript": "ENST00000916936.1",
"protein_id": "ENSP00000586995.1",
"transcript_support_level": null,
"aa_start": 215,
"aa_end": null,
"aa_length": 228,
"cds_start": 644,
"cds_end": null,
"cds_length": 687,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916936.1"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC5",
"gene_hgnc_id": 24662,
"hgvs_c": "c.575G>T",
"hgvs_p": "p.Arg192Leu",
"transcript": "ENST00000916938.1",
"protein_id": "ENSP00000586997.1",
"transcript_support_level": null,
"aa_start": 192,
"aa_end": null,
"aa_length": 205,
"cds_start": 575,
"cds_end": null,
"cds_length": 618,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916938.1"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC5",
"gene_hgnc_id": 24662,
"hgvs_c": "c.551G>T",
"hgvs_p": "p.Arg184Leu",
"transcript": "ENST00000596905.1",
"protein_id": "ENSP00000471002.1",
"transcript_support_level": 2,
"aa_start": 184,
"aa_end": null,
"aa_length": 197,
"cds_start": 551,
"cds_end": null,
"cds_length": 594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000596905.1"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC5",
"gene_hgnc_id": 24662,
"hgvs_c": "c.548G>T",
"hgvs_p": "p.Arg183Leu",
"transcript": "ENST00000916939.1",
"protein_id": "ENSP00000586998.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 196,
"cds_start": 548,
"cds_end": null,
"cds_length": 591,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916939.1"
},
{
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "EXOSC5",
"gene_hgnc_id": 24662,
"hgvs_c": "c.616-23G>T",
"hgvs_p": null,
"transcript": "ENST00000916940.1",
"protein_id": "ENSP00000586999.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 211,
"cds_start": null,
"cds_end": null,
"cds_length": 636,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916940.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "EXOSC5",
"gene_hgnc_id": 24662,
"hgvs_c": "c.243-117G>T",
"hgvs_p": null,
"transcript": "ENST00000602129.2",
"protein_id": "ENSP00000472396.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 86,
"cds_start": null,
"cds_end": null,
"cds_length": 261,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000602129.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC5",
"gene_hgnc_id": 24662,
"hgvs_c": "n.962G>T",
"hgvs_p": null,
"transcript": "ENST00000688768.1",
"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": "retained_intron",
"feature": "ENST00000688768.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000255730",
"gene_hgnc_id": null,
"hgvs_c": "n.351-23961C>A",
"hgvs_p": null,
"transcript": "ENST00000604424.1",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000604424.1"
}
],
"gene_symbol": "EXOSC5",
"gene_hgnc_id": 24662,
"dbsnp": "rs751654580",
"frequency_reference_population": 0.000004821189,
"hom_count_reference_population": 0,
"allele_count_reference_population": 7,
"gnomad_exomes_af": 0.00000482119,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.20788908004760742,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.15,
"revel_prediction": "Benign",
"alphamissense_score": 0.1245,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.38,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.394,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_020158.4",
"gene_symbol": "EXOSC5",
"hgnc_id": 24662,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.665G>T",
"hgvs_p": "p.Arg222Leu"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000540732.3",
"gene_symbol": "ENSG00000255730",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.210+8157C>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}