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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: 9-37784852-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=37784852&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 37784852,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_016042.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC3",
"gene_hgnc_id": 17944,
"hgvs_c": "c.193G>A",
"hgvs_p": "p.Val65Ile",
"transcript": "NM_016042.4",
"protein_id": "NP_057126.2",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 275,
"cds_start": 193,
"cds_end": null,
"cds_length": 828,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000327304.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_016042.4"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC3",
"gene_hgnc_id": 17944,
"hgvs_c": "c.193G>A",
"hgvs_p": "p.Val65Ile",
"transcript": "ENST00000327304.10",
"protein_id": "ENSP00000323046.4",
"transcript_support_level": 1,
"aa_start": 65,
"aa_end": null,
"aa_length": 275,
"cds_start": 193,
"cds_end": null,
"cds_length": 828,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_016042.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000327304.10"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "ENSG00000255872",
"gene_hgnc_id": null,
"hgvs_c": "n.*761-789G>A",
"hgvs_p": null,
"transcript": "ENST00000540557.1",
"protein_id": "ENSP00000457548.1",
"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": "ENST00000540557.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC3",
"gene_hgnc_id": 17944,
"hgvs_c": "c.193G>A",
"hgvs_p": "p.Val65Ile",
"transcript": "ENST00000858037.1",
"protein_id": "ENSP00000528096.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 275,
"cds_start": 193,
"cds_end": null,
"cds_length": 828,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858037.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC3",
"gene_hgnc_id": 17944,
"hgvs_c": "c.193G>A",
"hgvs_p": "p.Val65Ile",
"transcript": "ENST00000913387.1",
"protein_id": "ENSP00000583446.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 275,
"cds_start": 193,
"cds_end": null,
"cds_length": 828,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913387.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC3",
"gene_hgnc_id": 17944,
"hgvs_c": "c.193G>A",
"hgvs_p": "p.Val65Ile",
"transcript": "ENST00000956473.1",
"protein_id": "ENSP00000626532.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 275,
"cds_start": 193,
"cds_end": null,
"cds_length": 828,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000956473.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC3",
"gene_hgnc_id": 17944,
"hgvs_c": "c.193G>A",
"hgvs_p": "p.Val65Ile",
"transcript": "ENST00000913388.1",
"protein_id": "ENSP00000583447.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 273,
"cds_start": 193,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913388.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC3",
"gene_hgnc_id": 17944,
"hgvs_c": "c.193G>A",
"hgvs_p": "p.Val65Ile",
"transcript": "NM_001002269.2",
"protein_id": "NP_001002269.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 164,
"cds_start": 193,
"cds_end": null,
"cds_length": 495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001002269.2"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC3",
"gene_hgnc_id": 17944,
"hgvs_c": "c.193G>A",
"hgvs_p": "p.Val65Ile",
"transcript": "ENST00000396521.3",
"protein_id": "ENSP00000379775.3",
"transcript_support_level": 2,
"aa_start": 65,
"aa_end": null,
"aa_length": 164,
"cds_start": 193,
"cds_end": null,
"cds_length": 495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000396521.3"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC3",
"gene_hgnc_id": 17944,
"hgvs_c": "n.193G>A",
"hgvs_p": null,
"transcript": "ENST00000465229.5",
"protein_id": "ENSP00000418422.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000465229.5"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC3",
"gene_hgnc_id": 17944,
"hgvs_c": "n.213G>A",
"hgvs_p": null,
"transcript": "ENST00000678588.1",
"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": "ENST00000678588.1"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC3",
"gene_hgnc_id": 17944,
"hgvs_c": "n.193G>A",
"hgvs_p": null,
"transcript": "ENST00000679059.1",
"protein_id": "ENSP00000503947.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000679059.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "EXOSC3",
"gene_hgnc_id": 17944,
"hgvs_c": "n.86-789G>A",
"hgvs_p": null,
"transcript": "ENST00000482614.5",
"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": "ENST00000482614.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "EXOSC3",
"gene_hgnc_id": 17944,
"hgvs_c": "n.44-789G>A",
"hgvs_p": null,
"transcript": "ENST00000489414.5",
"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": "ENST00000489414.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "EXOSC3",
"gene_hgnc_id": 17944,
"hgvs_c": "n.-70-789G>A",
"hgvs_p": null,
"transcript": "ENST00000678095.1",
"protein_id": "ENSP00000503205.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000678095.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC3",
"gene_hgnc_id": 17944,
"hgvs_c": "n.-107G>A",
"hgvs_p": null,
"transcript": "ENST00000465860.6",
"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": "ENST00000465860.6"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EXOSC3",
"gene_hgnc_id": 17944,
"hgvs_c": "n.-139G>A",
"hgvs_p": null,
"transcript": "ENST00000490516.5",
"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": "pseudogene",
"feature": "ENST00000490516.5"
},
{
"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": "EXOSC3",
"gene_hgnc_id": 17944,
"hgvs_c": "n.-107G>A",
"hgvs_p": null,
"transcript": "ENST00000496910.1",
"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": "ENST00000496910.1"
}
],
"gene_symbol": "EXOSC3",
"gene_hgnc_id": 17944,
"dbsnp": "rs62640002",
"frequency_reference_population": 0.00038308266,
"hom_count_reference_population": 3,
"allele_count_reference_population": 616,
"gnomad_exomes_af": 0.000201972,
"gnomad_genomes_af": 0.00211339,
"gnomad_exomes_ac": 294,
"gnomad_genomes_ac": 322,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.009042143821716309,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.097,
"revel_prediction": "Benign",
"alphamissense_score": 0.1195,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.34,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.946,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP6,BS2_Supporting",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2_Supporting"
],
"verdict": "Likely_benign",
"transcript": "NM_016042.4",
"gene_symbol": "EXOSC3",
"hgnc_id": 17944,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.193G>A",
"hgvs_p": "p.Val65Ile"
},
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000540557.1",
"gene_symbol": "ENSG00000255872",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*761-789G>A",
"hgvs_p": null
}
],
"clinvar_disease": "EXOSC3-related disorder,Inborn genetic diseases,Pontocerebellar hypoplasia type 1B,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:4",
"phenotype_combined": "not specified|Pontocerebellar hypoplasia type 1B|EXOSC3-related disorder|not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}