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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: 1-175406219-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=175406219&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 175406219,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000367674.7",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNR",
"gene_hgnc_id": 11953,
"hgvs_c": "c.496A>G",
"hgvs_p": "p.Thr166Ala",
"transcript": "NM_003285.3",
"protein_id": "NP_003276.3",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 1358,
"cds_start": 496,
"cds_end": null,
"cds_length": 4077,
"cdna_start": 1030,
"cdna_end": null,
"cdna_length": 12774,
"mane_select": "ENST00000367674.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNR",
"gene_hgnc_id": 11953,
"hgvs_c": "c.496A>G",
"hgvs_p": "p.Thr166Ala",
"transcript": "ENST00000367674.7",
"protein_id": "ENSP00000356646.1",
"transcript_support_level": 5,
"aa_start": 166,
"aa_end": null,
"aa_length": 1358,
"cds_start": 496,
"cds_end": null,
"cds_length": 4077,
"cdna_start": 1030,
"cdna_end": null,
"cdna_length": 12774,
"mane_select": "NM_003285.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNR",
"gene_hgnc_id": 11953,
"hgvs_c": "c.496A>G",
"hgvs_p": "p.Thr166Ala",
"transcript": "ENST00000713954.1",
"protein_id": "ENSP00000519247.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 1304,
"cds_start": 496,
"cds_end": null,
"cds_length": 3915,
"cdna_start": 496,
"cdna_end": null,
"cdna_length": 12078,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNR",
"gene_hgnc_id": 11953,
"hgvs_c": "c.496A>G",
"hgvs_p": "p.Thr166Ala",
"transcript": "ENST00000713977.1",
"protein_id": "ENSP00000519268.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 1111,
"cds_start": 496,
"cds_end": null,
"cds_length": 3336,
"cdna_start": 660,
"cdna_end": null,
"cdna_length": 3643,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"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": "TNR",
"gene_hgnc_id": 11953,
"hgvs_c": "c.145A>G",
"hgvs_p": "p.Thr49Ala",
"transcript": "ENST00000422274.2",
"protein_id": "ENSP00000403413.2",
"transcript_support_level": 5,
"aa_start": 49,
"aa_end": null,
"aa_length": 178,
"cds_start": 145,
"cds_end": null,
"cds_length": 539,
"cdna_start": 146,
"cdna_end": null,
"cdna_length": 540,
"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": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNR",
"gene_hgnc_id": 11953,
"hgvs_c": "n.496A>G",
"hgvs_p": null,
"transcript": "ENST00000713955.1",
"protein_id": "ENSP00000519248.1",
"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": 5729,
"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": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNR",
"gene_hgnc_id": 11953,
"hgvs_c": "n.496A>G",
"hgvs_p": null,
"transcript": "ENST00000713978.1",
"protein_id": "ENSP00000519269.1",
"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": 2987,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNR",
"gene_hgnc_id": 11953,
"hgvs_c": "c.-400A>G",
"hgvs_p": null,
"transcript": "NM_001328635.2",
"protein_id": "NP_001315564.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1025,
"cds_start": -4,
"cds_end": null,
"cds_length": 3078,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12670,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TNR",
"gene_hgnc_id": 11953,
"dbsnp": "rs147204644",
"frequency_reference_population": 0.0046807276,
"hom_count_reference_population": 24,
"allele_count_reference_population": 7553,
"gnomad_exomes_af": 0.0047477,
"gnomad_genomes_af": 0.00403814,
"gnomad_exomes_ac": 6938,
"gnomad_genomes_ac": 615,
"gnomad_exomes_homalt": 22,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01012691855430603,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.33,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0666,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.28,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.788,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.05,
"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,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000367674.7",
"gene_symbol": "TNR",
"hgnc_id": 11953,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.496A>G",
"hgvs_p": "p.Thr166Ala"
}
],
"clinvar_disease": "Inborn genetic diseases,Parkinson disease,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2 B:1",
"phenotype_combined": "Parkinson disease|not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}