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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: 3-81537080-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=81537080&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 81537080,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000429644.7",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"hgvs_c": "c.1634A>G",
"hgvs_p": "p.His545Arg",
"transcript": "NM_000158.4",
"protein_id": "NP_000149.4",
"transcript_support_level": null,
"aa_start": 545,
"aa_end": null,
"aa_length": 702,
"cds_start": 1634,
"cds_end": null,
"cds_length": 2109,
"cdna_start": 1762,
"cdna_end": null,
"cdna_length": 2941,
"mane_select": "ENST00000429644.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"hgvs_c": "c.1634A>G",
"hgvs_p": "p.His545Arg",
"transcript": "ENST00000429644.7",
"protein_id": "ENSP00000410833.2",
"transcript_support_level": 1,
"aa_start": 545,
"aa_end": null,
"aa_length": 702,
"cds_start": 1634,
"cds_end": null,
"cds_length": 2109,
"cdna_start": 1762,
"cdna_end": null,
"cdna_length": 2941,
"mane_select": "NM_000158.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"hgvs_c": "c.1511A>G",
"hgvs_p": "p.His504Arg",
"transcript": "ENST00000489715.1",
"protein_id": "ENSP00000419638.1",
"transcript_support_level": 2,
"aa_start": 504,
"aa_end": null,
"aa_length": 661,
"cds_start": 1511,
"cds_end": null,
"cds_length": 1986,
"cdna_start": 1564,
"cdna_end": null,
"cdna_length": 2513,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"hgvs_c": "n.35A>G",
"hgvs_p": null,
"transcript": "ENST00000484687.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 863,
"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": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"hgvs_c": "n.1762A>G",
"hgvs_p": null,
"transcript": "XR_007095662.1",
"protein_id": null,
"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": 8416,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"dbsnp": "rs137852889",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9677695631980896,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.947,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9933,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.52,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.608,
"phylop100way_prediction": "Pathogenic",
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PP3_Strong,PP5_Moderate",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM1",
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000429644.7",
"gene_symbol": "GBE1",
"hgnc_id": 4180,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1634A>G",
"hgvs_p": "p.His545Arg"
}
],
"clinvar_disease": " classic hepatic, fatal perinatal neuromuscular form, type IV,Glycogen storage disease,Glycogen storage disease IV,Glycogen storage disease due to glycogen branching enzyme deficiency",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Glycogen storage disease due to glycogen branching enzyme deficiency, fatal perinatal neuromuscular form|Glycogen storage disease, type IV|Glycogen storage disease, type IV;Glycogen storage disease IV, classic hepatic",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}