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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: 13-27569067-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=27569067&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 27569067,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000316334.5",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LNX2",
"gene_hgnc_id": 20421,
"hgvs_c": "c.617T>G",
"hgvs_p": "p.Leu206Arg",
"transcript": "NM_153371.4",
"protein_id": "NP_699202.1",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 690,
"cds_start": 617,
"cds_end": null,
"cds_length": 2073,
"cdna_start": 872,
"cdna_end": null,
"cdna_length": 4750,
"mane_select": "ENST00000316334.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LNX2",
"gene_hgnc_id": 20421,
"hgvs_c": "c.617T>G",
"hgvs_p": "p.Leu206Arg",
"transcript": "ENST00000316334.5",
"protein_id": "ENSP00000325929.3",
"transcript_support_level": 1,
"aa_start": 206,
"aa_end": null,
"aa_length": 690,
"cds_start": 617,
"cds_end": null,
"cds_length": 2073,
"cdna_start": 872,
"cdna_end": null,
"cdna_length": 4750,
"mane_select": "NM_153371.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LNX2",
"gene_hgnc_id": 20421,
"hgvs_c": "c.617T>G",
"hgvs_p": "p.Leu206Arg",
"transcript": "ENST00000649248.1",
"protein_id": "ENSP00000497224.1",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 690,
"cds_start": 617,
"cds_end": null,
"cds_length": 2073,
"cdna_start": 782,
"cdna_end": null,
"cdna_length": 4648,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LNX2",
"gene_hgnc_id": 20421,
"hgvs_c": "c.617T>G",
"hgvs_p": "p.Leu206Arg",
"transcript": "XM_017020434.2",
"protein_id": "XP_016875923.1",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 690,
"cds_start": 617,
"cds_end": null,
"cds_length": 2073,
"cdna_start": 786,
"cdna_end": null,
"cdna_length": 4664,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LNX2",
"gene_hgnc_id": 20421,
"hgvs_c": "c.617T>G",
"hgvs_p": "p.Leu206Arg",
"transcript": "XM_047430145.1",
"protein_id": "XP_047286101.1",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 690,
"cds_start": 617,
"cds_end": null,
"cds_length": 2073,
"cdna_start": 1229,
"cdna_end": null,
"cdna_length": 5107,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LNX2",
"gene_hgnc_id": 20421,
"hgvs_c": "c.617T>G",
"hgvs_p": "p.Leu206Arg",
"transcript": "XM_047430147.1",
"protein_id": "XP_047286103.1",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 690,
"cds_start": 617,
"cds_end": null,
"cds_length": 2073,
"cdna_start": 12750,
"cdna_end": null,
"cdna_length": 16628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LNX2",
"gene_hgnc_id": 20421,
"hgvs_c": "c.617T>G",
"hgvs_p": "p.Leu206Arg",
"transcript": "XM_047430148.1",
"protein_id": "XP_047286104.1",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 690,
"cds_start": 617,
"cds_end": null,
"cds_length": 2073,
"cdna_start": 937,
"cdna_end": null,
"cdna_length": 4815,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LNX2",
"gene_hgnc_id": 20421,
"hgvs_c": "c.617T>G",
"hgvs_p": "p.Leu206Arg",
"transcript": "XM_047430149.1",
"protein_id": "XP_047286105.1",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 690,
"cds_start": 617,
"cds_end": null,
"cds_length": 2073,
"cdna_start": 1394,
"cdna_end": null,
"cdna_length": 5272,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LNX2",
"gene_hgnc_id": 20421,
"hgvs_c": "c.617T>G",
"hgvs_p": "p.Leu206Arg",
"transcript": "XM_047430150.1",
"protein_id": "XP_047286106.1",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 690,
"cds_start": 617,
"cds_end": null,
"cds_length": 2073,
"cdna_start": 1224,
"cdna_end": null,
"cdna_length": 5102,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LNX2",
"gene_hgnc_id": 20421,
"hgvs_c": "c.617T>G",
"hgvs_p": "p.Leu206Arg",
"transcript": "XM_011534995.3",
"protein_id": "XP_011533297.1",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 567,
"cds_start": 617,
"cds_end": null,
"cds_length": 1704,
"cdna_start": 872,
"cdna_end": null,
"cdna_length": 4381,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LNX2",
"gene_hgnc_id": 20421,
"hgvs_c": "c.617T>G",
"hgvs_p": "p.Leu206Arg",
"transcript": "XM_047430151.1",
"protein_id": "XP_047286107.1",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 567,
"cds_start": 617,
"cds_end": null,
"cds_length": 1704,
"cdna_start": 1229,
"cdna_end": null,
"cdna_length": 4738,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LNX2",
"gene_hgnc_id": 20421,
"dbsnp": "rs758811088",
"frequency_reference_population": 0.000011631137,
"hom_count_reference_population": 0,
"allele_count_reference_population": 17,
"gnomad_exomes_af": 0.0000116311,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 17,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.49934545159339905,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.194,
"revel_prediction": "Benign",
"alphamissense_score": 0.1214,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.34,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 8.867,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000316334.5",
"gene_symbol": "LNX2",
"hgnc_id": 20421,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.617T>G",
"hgvs_p": "p.Leu206Arg"
}
],
"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
}