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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: 1-110401561-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=110401561&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 110401561,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_006402.3",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMTOR5",
"gene_hgnc_id": 17955,
"hgvs_c": "c.238G>C",
"hgvs_p": "p.Asp80His",
"transcript": "NM_001382293.1",
"protein_id": "NP_001369222.1",
"transcript_support_level": null,
"aa_start": 80,
"aa_end": null,
"aa_length": 91,
"cds_start": 238,
"cds_end": null,
"cds_length": 276,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000602318.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001382293.1"
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMTOR5",
"gene_hgnc_id": 17955,
"hgvs_c": "c.238G>C",
"hgvs_p": "p.Asp80His",
"transcript": "ENST00000602318.6",
"protein_id": "ENSP00000473439.1",
"transcript_support_level": 1,
"aa_start": 80,
"aa_end": null,
"aa_length": 91,
"cds_start": 238,
"cds_end": null,
"cds_length": 276,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001382293.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000602318.6"
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMTOR5",
"gene_hgnc_id": 17955,
"hgvs_c": "c.484G>C",
"hgvs_p": "p.Asp162His",
"transcript": "ENST00000256644.8",
"protein_id": "ENSP00000256644.4",
"transcript_support_level": 1,
"aa_start": 162,
"aa_end": null,
"aa_length": 173,
"cds_start": 484,
"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": "ENST00000256644.8"
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMTOR5",
"gene_hgnc_id": 17955,
"hgvs_c": "c.484G>C",
"hgvs_p": "p.Asp162His",
"transcript": "NM_006402.3",
"protein_id": "NP_006393.2",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 173,
"cds_start": 484,
"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": "NM_006402.3"
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMTOR5",
"gene_hgnc_id": 17955,
"hgvs_c": "c.235G>C",
"hgvs_p": "p.Asp79His",
"transcript": "ENST00000474861.6",
"protein_id": "ENSP00000434828.1",
"transcript_support_level": 2,
"aa_start": 79,
"aa_end": null,
"aa_length": 90,
"cds_start": 235,
"cds_end": null,
"cds_length": 273,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000474861.6"
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMTOR5",
"gene_hgnc_id": 17955,
"hgvs_c": "c.235G>C",
"hgvs_p": "p.Asp79His",
"transcript": "ENST00000483260.5",
"protein_id": "ENSP00000435085.1",
"transcript_support_level": 2,
"aa_start": 79,
"aa_end": null,
"aa_length": 90,
"cds_start": 235,
"cds_end": null,
"cds_length": 273,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000483260.5"
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMTOR5",
"gene_hgnc_id": 17955,
"hgvs_c": "c.235G>C",
"hgvs_p": "p.Asp79His",
"transcript": "ENST00000872833.1",
"protein_id": "ENSP00000542892.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 90,
"cds_start": 235,
"cds_end": null,
"cds_length": 273,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872833.1"
},
{
"aa_ref": "D",
"aa_alt": "H",
"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": "LAMTOR5",
"gene_hgnc_id": 17955,
"hgvs_c": "c.202G>C",
"hgvs_p": "p.Asp68His",
"transcript": "ENST00000602858.5",
"protein_id": "ENSP00000473357.1",
"transcript_support_level": 2,
"aa_start": 68,
"aa_end": null,
"aa_length": 79,
"cds_start": 202,
"cds_end": null,
"cds_length": 240,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000602858.5"
},
{
"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": "LAMTOR5",
"gene_hgnc_id": 17955,
"hgvs_c": "n.1518G>C",
"hgvs_p": null,
"transcript": "ENST00000464240.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000464240.1"
},
{
"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": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LAMTOR5-AS1",
"gene_hgnc_id": 40823,
"hgvs_c": "n.183-10612C>G",
"hgvs_p": null,
"transcript": "ENST00000590413.5",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000590413.5"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LAMTOR5-AS1",
"gene_hgnc_id": 40823,
"hgvs_c": "n.929-16686C>G",
"hgvs_p": null,
"transcript": "ENST00000626572.2",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000626572.2"
}
],
"gene_symbol": "LAMTOR5",
"gene_hgnc_id": 17955,
"dbsnp": "rs780723150",
"frequency_reference_population": 0.0000013748898,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000137489,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.37804466485977173,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.213,
"revel_prediction": "Benign",
"alphamissense_score": 0.4805,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.13,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.092,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_006402.3",
"gene_symbol": "LAMTOR5",
"hgnc_id": 17955,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.484G>C",
"hgvs_p": "p.Asp162His"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000590413.5",
"gene_symbol": "LAMTOR5-AS1",
"hgnc_id": 40823,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.183-10612C>G",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}