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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: 3-49121322-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=49121322&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 49121322,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_002292.4",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMB2",
"gene_hgnc_id": 6487,
"hgvs_c": "c.5301G>A",
"hgvs_p": "p.Glu1767Glu",
"transcript": "NM_002292.4",
"protein_id": "NP_002283.3",
"transcript_support_level": null,
"aa_start": 1767,
"aa_end": null,
"aa_length": 1798,
"cds_start": 5301,
"cds_end": null,
"cds_length": 5397,
"cdna_start": 5484,
"cdna_end": null,
"cdna_length": 5692,
"mane_select": "ENST00000305544.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMB2",
"gene_hgnc_id": 6487,
"hgvs_c": "c.5301G>A",
"hgvs_p": "p.Glu1767Glu",
"transcript": "ENST00000305544.9",
"protein_id": "ENSP00000307156.4",
"transcript_support_level": 1,
"aa_start": 1767,
"aa_end": null,
"aa_length": 1798,
"cds_start": 5301,
"cds_end": null,
"cds_length": 5397,
"cdna_start": 5484,
"cdna_end": null,
"cdna_length": 5692,
"mane_select": "NM_002292.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMB2",
"gene_hgnc_id": 6487,
"hgvs_c": "c.5301G>A",
"hgvs_p": "p.Glu1767Glu",
"transcript": "ENST00000418109.5",
"protein_id": "ENSP00000388325.1",
"transcript_support_level": 1,
"aa_start": 1767,
"aa_end": null,
"aa_length": 1798,
"cds_start": 5301,
"cds_end": null,
"cds_length": 5397,
"cdna_start": 5466,
"cdna_end": null,
"cdna_length": 5674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMB2",
"gene_hgnc_id": 6487,
"hgvs_c": "c.5301G>A",
"hgvs_p": "p.Glu1767Glu",
"transcript": "XM_005265127.5",
"protein_id": "XP_005265184.1",
"transcript_support_level": null,
"aa_start": 1767,
"aa_end": null,
"aa_length": 1798,
"cds_start": 5301,
"cds_end": null,
"cds_length": 5397,
"cdna_start": 5398,
"cdna_end": null,
"cdna_length": 5606,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMB2",
"gene_hgnc_id": 6487,
"hgvs_c": "n.481G>A",
"hgvs_p": null,
"transcript": "ENST00000467506.5",
"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": 689,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMB2",
"gene_hgnc_id": 6487,
"hgvs_c": "n.205G>A",
"hgvs_p": null,
"transcript": "ENST00000484713.1",
"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": 412,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMB2",
"gene_hgnc_id": 6487,
"hgvs_c": "n.956G>A",
"hgvs_p": null,
"transcript": "ENST00000498377.1",
"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": 1021,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LAMB2",
"gene_hgnc_id": 6487,
"dbsnp": "rs2045222604",
"frequency_reference_population": 0.000003098262,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000273675,
"gnomad_genomes_af": 0.00000656935,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.44999998807907104,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.45,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.353,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_002292.4",
"gene_symbol": "LAMB2",
"hgnc_id": 6487,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.5301G>A",
"hgvs_p": "p.Glu1767Glu"
}
],
"clinvar_disease": "LAMB2-related infantile-onset nephrotic syndrome,Pierson syndrome",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "LAMB2-related infantile-onset nephrotic syndrome;Pierson syndrome",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}