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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: 3-133757854-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=133757854&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 133757854,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000402696.9",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.956A>G",
"hgvs_p": "p.His319Arg",
"transcript": "NM_001063.4",
"protein_id": "NP_001054.2",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 698,
"cds_start": 956,
"cds_end": null,
"cds_length": 2097,
"cdna_start": 1004,
"cdna_end": null,
"cdna_length": 20166,
"mane_select": "ENST00000402696.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.956A>G",
"hgvs_p": "p.His319Arg",
"transcript": "ENST00000402696.9",
"protein_id": "ENSP00000385834.3",
"transcript_support_level": 1,
"aa_start": 319,
"aa_end": null,
"aa_length": 698,
"cds_start": 956,
"cds_end": null,
"cds_length": 2097,
"cdna_start": 1004,
"cdna_end": null,
"cdna_length": 20166,
"mane_select": "NM_001063.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.824A>G",
"hgvs_p": "p.His275Arg",
"transcript": "NM_001354703.2",
"protein_id": "NP_001341632.2",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 654,
"cds_start": 824,
"cds_end": null,
"cds_length": 1965,
"cdna_start": 1972,
"cdna_end": null,
"cdna_length": 21134,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.575A>G",
"hgvs_p": "p.His192Arg",
"transcript": "NM_001354704.2",
"protein_id": "NP_001341633.2",
"transcript_support_level": null,
"aa_start": 192,
"aa_end": null,
"aa_length": 571,
"cds_start": 575,
"cds_end": null,
"cds_length": 1716,
"cdna_start": 831,
"cdna_end": null,
"cdna_length": 19993,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "n.*12A>G",
"hgvs_p": null,
"transcript": "ENST00000485977.1",
"protein_id": "ENSP00000418716.1",
"transcript_support_level": 3,
"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": 580,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "n.*12A>G",
"hgvs_p": null,
"transcript": "ENST00000485977.1",
"protein_id": "ENSP00000418716.1",
"transcript_support_level": 3,
"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": 580,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"dbsnp": "rs41295774",
"frequency_reference_population": 0.0012228922,
"hom_count_reference_population": 17,
"allele_count_reference_population": 1974,
"gnomad_exomes_af": 0.00109379,
"gnomad_genomes_af": 0.00246192,
"gnomad_exomes_ac": 1599,
"gnomad_genomes_ac": 375,
"gnomad_exomes_homalt": 16,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.05692121386528015,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.037,
"revel_prediction": "Benign",
"alphamissense_score": 0.0668,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.74,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.7,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000402696.9",
"gene_symbol": "TF",
"hgnc_id": 11740,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.956A>G",
"hgvs_p": "p.His319Arg"
}
],
"clinvar_disease": "Atransferrinemia,Transferrin variant D(Chi),not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "Transferrin variant D(Chi)|Atransferrinemia|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}