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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: 3-50287140-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=50287140&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 50287140,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_153215.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LSMEM2",
"gene_hgnc_id": 26781,
"hgvs_c": "c.433C>T",
"hgvs_p": "p.Arg145Cys",
"transcript": "NM_153215.3",
"protein_id": "NP_694947.1",
"transcript_support_level": null,
"aa_start": 145,
"aa_end": null,
"aa_length": 164,
"cds_start": 433,
"cds_end": null,
"cds_length": 495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000316436.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_153215.3"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LSMEM2",
"gene_hgnc_id": 26781,
"hgvs_c": "c.433C>T",
"hgvs_p": "p.Arg145Cys",
"transcript": "ENST00000316436.4",
"protein_id": "ENSP00000315081.3",
"transcript_support_level": 1,
"aa_start": 145,
"aa_end": null,
"aa_length": 164,
"cds_start": 433,
"cds_end": null,
"cds_length": 495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_153215.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000316436.4"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LSMEM2",
"gene_hgnc_id": 26781,
"hgvs_c": "c.451C>T",
"hgvs_p": "p.Arg151Cys",
"transcript": "ENST00000948603.1",
"protein_id": "ENSP00000618662.1",
"transcript_support_level": null,
"aa_start": 151,
"aa_end": null,
"aa_length": 170,
"cds_start": 451,
"cds_end": null,
"cds_length": 513,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948603.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LSMEM2",
"gene_hgnc_id": 26781,
"hgvs_c": "c.430C>T",
"hgvs_p": "p.Arg144Cys",
"transcript": "NM_001304385.2",
"protein_id": "NP_001291314.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 163,
"cds_start": 430,
"cds_end": null,
"cds_length": 492,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001304385.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LSMEM2",
"gene_hgnc_id": 26781,
"hgvs_c": "c.430C>T",
"hgvs_p": "p.Arg144Cys",
"transcript": "ENST00000878856.1",
"protein_id": "ENSP00000548915.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 163,
"cds_start": 430,
"cds_end": null,
"cds_length": 492,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000878856.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LSMEM2",
"gene_hgnc_id": 26781,
"hgvs_c": "c.244C>T",
"hgvs_p": "p.Arg82Cys",
"transcript": "ENST00000948602.1",
"protein_id": "ENSP00000618661.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 101,
"cds_start": 244,
"cds_end": null,
"cds_length": 306,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948602.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LSMEM2",
"gene_hgnc_id": 26781,
"hgvs_c": "c.460C>T",
"hgvs_p": "p.Arg154Cys",
"transcript": "XM_006712979.5",
"protein_id": "XP_006713042.1",
"transcript_support_level": null,
"aa_start": 154,
"aa_end": null,
"aa_length": 173,
"cds_start": 460,
"cds_end": null,
"cds_length": 522,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006712979.5"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LSMEM2",
"gene_hgnc_id": 26781,
"hgvs_c": "c.457C>T",
"hgvs_p": "p.Arg153Cys",
"transcript": "XM_006712980.5",
"protein_id": "XP_006713043.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 172,
"cds_start": 457,
"cds_end": null,
"cds_length": 519,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006712980.5"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LSMEM2",
"gene_hgnc_id": 26781,
"hgvs_c": "c.361C>T",
"hgvs_p": "p.Arg121Cys",
"transcript": "XM_011533370.4",
"protein_id": "XP_011531672.1",
"transcript_support_level": null,
"aa_start": 121,
"aa_end": null,
"aa_length": 140,
"cds_start": 361,
"cds_end": null,
"cds_length": 423,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533370.4"
}
],
"gene_symbol": "LSMEM2",
"gene_hgnc_id": 26781,
"dbsnp": "rs782665715",
"frequency_reference_population": 0.00016108846,
"hom_count_reference_population": 2,
"allele_count_reference_population": 260,
"gnomad_exomes_af": 0.000171017,
"gnomad_genomes_af": 0.0000657142,
"gnomad_exomes_ac": 250,
"gnomad_genomes_ac": 10,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.43122169375419617,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.257,
"revel_prediction": "Benign",
"alphamissense_score": 0.5898,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.09,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 1.808,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_153215.3",
"gene_symbol": "LSMEM2",
"hgnc_id": 26781,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.433C>T",
"hgvs_p": "p.Arg145Cys"
}
],
"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
}