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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: 3-54918638-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=54918638&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 54918638,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_020678.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRTM1",
"gene_hgnc_id": 25023,
"hgvs_c": "c.859G>T",
"hgvs_p": "p.Ala287Ser",
"transcript": "NM_020678.4",
"protein_id": "NP_065729.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 345,
"cds_start": 859,
"cds_end": null,
"cds_length": 1038,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000273286.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_020678.4"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRTM1",
"gene_hgnc_id": 25023,
"hgvs_c": "c.859G>T",
"hgvs_p": "p.Ala287Ser",
"transcript": "ENST00000273286.6",
"protein_id": "ENSP00000273286.5",
"transcript_support_level": 1,
"aa_start": 287,
"aa_end": null,
"aa_length": 345,
"cds_start": 859,
"cds_end": null,
"cds_length": 1038,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_020678.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000273286.6"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRTM1",
"gene_hgnc_id": 25023,
"hgvs_c": "c.631G>T",
"hgvs_p": "p.Ala211Ser",
"transcript": "ENST00000493075.1",
"protein_id": "ENSP00000419772.1",
"transcript_support_level": 1,
"aa_start": 211,
"aa_end": null,
"aa_length": 269,
"cds_start": 631,
"cds_end": null,
"cds_length": 810,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000493075.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": 27,
"intron_rank_end": null,
"gene_symbol": "CACNA2D3",
"gene_hgnc_id": 15460,
"hgvs_c": "c.2449+18770C>A",
"hgvs_p": null,
"transcript": "NM_018398.3",
"protein_id": "NP_060868.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1091,
"cds_start": null,
"cds_end": null,
"cds_length": 3276,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000474759.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018398.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": 27,
"intron_rank_end": null,
"gene_symbol": "CACNA2D3",
"gene_hgnc_id": 15460,
"hgvs_c": "c.2449+18770C>A",
"hgvs_p": null,
"transcript": "ENST00000474759.6",
"protein_id": "ENSP00000419101.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1091,
"cds_start": null,
"cds_end": null,
"cds_length": 3276,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_018398.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000474759.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "CACNA2D3",
"gene_hgnc_id": 15460,
"hgvs_c": "c.2167+18770C>A",
"hgvs_p": null,
"transcript": "ENST00000490478.5",
"protein_id": "ENSP00000417279.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 997,
"cds_start": null,
"cds_end": null,
"cds_length": 2994,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000490478.5"
},
{
"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": 35,
"intron_rank": 24,
"intron_rank_end": null,
"gene_symbol": "CACNA2D3",
"gene_hgnc_id": 15460,
"hgvs_c": "n.*527+18770C>A",
"hgvs_p": null,
"transcript": "ENST00000471363.5",
"protein_id": "ENSP00000418228.1",
"transcript_support_level": 1,
"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": "ENST00000471363.5"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRTM1",
"gene_hgnc_id": 25023,
"hgvs_c": "c.631G>T",
"hgvs_p": "p.Ala211Ser",
"transcript": "NM_001304389.2",
"protein_id": "NP_001291318.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 269,
"cds_start": 631,
"cds_end": null,
"cds_length": 810,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001304389.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "CACNA2D3",
"gene_hgnc_id": 15460,
"hgvs_c": "c.2431+18770C>A",
"hgvs_p": null,
"transcript": "ENST00000958523.1",
"protein_id": "ENSP00000628582.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1085,
"cds_start": null,
"cds_end": null,
"cds_length": 3258,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958523.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "CACNA2D3",
"gene_hgnc_id": 15460,
"hgvs_c": "c.2341+18770C>A",
"hgvs_p": null,
"transcript": "ENST00000958525.1",
"protein_id": "ENSP00000628584.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1055,
"cds_start": null,
"cds_end": null,
"cds_length": 3168,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958525.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "CACNA2D3",
"gene_hgnc_id": 15460,
"hgvs_c": "c.2305+18770C>A",
"hgvs_p": null,
"transcript": "ENST00000958524.1",
"protein_id": "ENSP00000628583.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1043,
"cds_start": null,
"cds_end": null,
"cds_length": 3132,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958524.1"
}
],
"gene_symbol": "LRTM1",
"gene_hgnc_id": 25023,
"dbsnp": "rs200994023",
"frequency_reference_population": 0.00009107423,
"hom_count_reference_population": 1,
"allele_count_reference_population": 147,
"gnomad_exomes_af": 0.0000868738,
"gnomad_genomes_af": 0.000131425,
"gnomad_exomes_ac": 127,
"gnomad_genomes_ac": 20,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.10516706109046936,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.21,
"revel_prediction": "Benign",
"alphamissense_score": 0.1353,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.36,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.565,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_020678.4",
"gene_symbol": "LRTM1",
"hgnc_id": 25023,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.859G>T",
"hgvs_p": "p.Ala287Ser"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_018398.3",
"gene_symbol": "CACNA2D3",
"hgnc_id": 15460,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.2449+18770C>A",
"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
}