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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: 19-54115453-AC-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=54115453&ref=AC&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 54115453,
"ref": "AC",
"alt": "A",
"effect": "5_prime_UTR_variant",
"transcript": "NM_013342.4",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFPT",
"gene_hgnc_id": 13630,
"hgvs_c": "c.-185delG",
"hgvs_p": null,
"transcript": "NM_013342.4",
"protein_id": "NP_037474.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 253,
"cds_start": null,
"cds_end": null,
"cds_length": 762,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000391759.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_013342.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFPT",
"gene_hgnc_id": 13630,
"hgvs_c": "c.-185delG",
"hgvs_p": null,
"transcript": "ENST00000391759.6",
"protein_id": "ENSP00000375639.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 253,
"cds_start": null,
"cds_end": null,
"cds_length": 762,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_013342.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000391759.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPF31",
"gene_hgnc_id": 15446,
"hgvs_c": "c.-349delC",
"hgvs_p": null,
"transcript": "ENST00000419967.5",
"protein_id": "ENSP00000405166.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 491,
"cds_start": null,
"cds_end": null,
"cds_length": 1476,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000419967.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFPT",
"gene_hgnc_id": 13630,
"hgvs_c": "c.-185delG",
"hgvs_p": null,
"transcript": "ENST00000911296.1",
"protein_id": "ENSP00000581355.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 270,
"cds_start": null,
"cds_end": null,
"cds_length": 813,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911296.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFPT",
"gene_hgnc_id": 13630,
"hgvs_c": "c.-185delG",
"hgvs_p": null,
"transcript": "ENST00000911297.1",
"protein_id": "ENSP00000581356.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 251,
"cds_start": null,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911297.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFPT",
"gene_hgnc_id": 13630,
"hgvs_c": "c.-185delG",
"hgvs_p": null,
"transcript": "ENST00000391757.1",
"protein_id": "ENSP00000375637.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 193,
"cds_start": null,
"cds_end": null,
"cds_length": 582,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000391757.1"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFPT",
"gene_hgnc_id": 13630,
"hgvs_c": "n.-185delG",
"hgvs_p": null,
"transcript": "ENST00000420715.6",
"protein_id": "ENSP00000395180.1",
"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": "ENST00000420715.6"
}
],
"gene_symbol": "TFPT",
"gene_hgnc_id": 13630,
"dbsnp": "rs773806123",
"frequency_reference_population": 0.0003223879,
"hom_count_reference_population": 0,
"allele_count_reference_population": 232,
"gnomad_exomes_af": 0.000318817,
"gnomad_genomes_af": 0.000335734,
"gnomad_exomes_ac": 181,
"gnomad_genomes_ac": 51,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"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": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": -0.724,
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP6",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BP6"
],
"verdict": "Likely_benign",
"transcript": "NM_013342.4",
"gene_symbol": "TFPT",
"hgnc_id": 13630,
"effects": [
"5_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-185delG",
"hgvs_p": null
},
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000419967.5",
"gene_symbol": "PRPF31",
"hgnc_id": 15446,
"effects": [
"5_prime_UTR_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.-349delC",
"hgvs_p": null
}
],
"clinvar_disease": "PRPF31-related disorder",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "PRPF31-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}