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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: 2-140238223-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=140238223&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 140238223,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_018557.3",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 89,
"exon_rank_end": null,
"exon_count": 91,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP1B",
"gene_hgnc_id": 6693,
"hgvs_c": "c.13489A>C",
"hgvs_p": "p.Met4497Leu",
"transcript": "NM_018557.3",
"protein_id": "NP_061027.2",
"transcript_support_level": null,
"aa_start": 4497,
"aa_end": null,
"aa_length": 4599,
"cds_start": 13489,
"cds_end": null,
"cds_length": 13800,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000389484.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018557.3"
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 89,
"exon_rank_end": null,
"exon_count": 91,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP1B",
"gene_hgnc_id": 6693,
"hgvs_c": "c.13489A>C",
"hgvs_p": "p.Met4497Leu",
"transcript": "ENST00000389484.8",
"protein_id": "ENSP00000374135.3",
"transcript_support_level": 1,
"aa_start": 4497,
"aa_end": null,
"aa_length": 4599,
"cds_start": 13489,
"cds_end": null,
"cds_length": 13800,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_018557.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000389484.8"
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP1B",
"gene_hgnc_id": 6693,
"hgvs_c": "c.2182A>C",
"hgvs_p": "p.Met728Leu",
"transcript": "ENST00000437977.5",
"protein_id": "ENSP00000415052.1",
"transcript_support_level": 5,
"aa_start": 728,
"aa_end": null,
"aa_length": 797,
"cds_start": 2182,
"cds_end": null,
"cds_length": 2394,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000437977.5"
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP1B",
"gene_hgnc_id": 6693,
"hgvs_c": "c.796A>C",
"hgvs_p": "p.Met266Leu",
"transcript": "ENST00000442974.1",
"protein_id": "ENSP00000393859.1",
"transcript_support_level": 5,
"aa_start": 266,
"aa_end": null,
"aa_length": 278,
"cds_start": 796,
"cds_end": null,
"cds_length": 837,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000442974.1"
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 89,
"exon_rank_end": null,
"exon_count": 91,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP1B",
"gene_hgnc_id": 6693,
"hgvs_c": "c.13099A>C",
"hgvs_p": "p.Met4367Leu",
"transcript": "XM_017004341.2",
"protein_id": "XP_016859830.1",
"transcript_support_level": null,
"aa_start": 4367,
"aa_end": null,
"aa_length": 4469,
"cds_start": 13099,
"cds_end": null,
"cds_length": 13410,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017004341.2"
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 60,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP1B",
"gene_hgnc_id": 6693,
"hgvs_c": "c.8341A>C",
"hgvs_p": "p.Met2781Leu",
"transcript": "XM_017004342.1",
"protein_id": "XP_016859831.1",
"transcript_support_level": null,
"aa_start": 2781,
"aa_end": null,
"aa_length": 2883,
"cds_start": 8341,
"cds_end": null,
"cds_length": 8652,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017004342.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000300471",
"gene_hgnc_id": null,
"hgvs_c": "n.104+13345T>G",
"hgvs_p": null,
"transcript": "ENST00000772126.1",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "ENST00000772126.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000300471",
"gene_hgnc_id": null,
"hgvs_c": "n.135+13345T>G",
"hgvs_p": null,
"transcript": "ENST00000772127.1",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "ENST00000772127.1"
}
],
"gene_symbol": "LRP1B",
"gene_hgnc_id": 6693,
"dbsnp": "rs749162634",
"frequency_reference_population": 0.0000043727537,
"hom_count_reference_population": 0,
"allele_count_reference_population": 7,
"gnomad_exomes_af": 0.00000344859,
"gnomad_genomes_af": 0.0000132489,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.30539870262145996,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.11,
"revel_prediction": "Benign",
"alphamissense_score": 0.3994,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.33,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.645,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.03,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4,BS2",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_018557.3",
"gene_symbol": "LRP1B",
"hgnc_id": 6693,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.13489A>C",
"hgvs_p": "p.Met4497Leu"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000772126.1",
"gene_symbol": "ENSG00000300471",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.104+13345T>G",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}