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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: 5-1474569-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=1474569&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 1474569,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_024830.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LPCAT1",
"gene_hgnc_id": 25718,
"hgvs_c": "c.1016G>A",
"hgvs_p": "p.Arg339Gln",
"transcript": "NM_024830.5",
"protein_id": "NP_079106.3",
"transcript_support_level": null,
"aa_start": 339,
"aa_end": null,
"aa_length": 534,
"cds_start": 1016,
"cds_end": null,
"cds_length": 1605,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000283415.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024830.5"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LPCAT1",
"gene_hgnc_id": 25718,
"hgvs_c": "c.1016G>A",
"hgvs_p": "p.Arg339Gln",
"transcript": "ENST00000283415.4",
"protein_id": "ENSP00000283415.3",
"transcript_support_level": 1,
"aa_start": 339,
"aa_end": null,
"aa_length": 534,
"cds_start": 1016,
"cds_end": null,
"cds_length": 1605,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_024830.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000283415.4"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LPCAT1",
"gene_hgnc_id": 25718,
"hgvs_c": "c.1112G>A",
"hgvs_p": "p.Arg371Gln",
"transcript": "ENST00000934191.1",
"protein_id": "ENSP00000604250.1",
"transcript_support_level": null,
"aa_start": 371,
"aa_end": null,
"aa_length": 566,
"cds_start": 1112,
"cds_end": null,
"cds_length": 1701,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934191.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LPCAT1",
"gene_hgnc_id": 25718,
"hgvs_c": "c.1103G>A",
"hgvs_p": "p.Arg368Gln",
"transcript": "ENST00000934189.1",
"protein_id": "ENSP00000604248.1",
"transcript_support_level": null,
"aa_start": 368,
"aa_end": null,
"aa_length": 563,
"cds_start": 1103,
"cds_end": null,
"cds_length": 1692,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934189.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LPCAT1",
"gene_hgnc_id": 25718,
"hgvs_c": "c.1016G>A",
"hgvs_p": "p.Arg339Gln",
"transcript": "ENST00000934190.1",
"protein_id": "ENSP00000604249.1",
"transcript_support_level": null,
"aa_start": 339,
"aa_end": null,
"aa_length": 538,
"cds_start": 1016,
"cds_end": null,
"cds_length": 1617,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934190.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LPCAT1",
"gene_hgnc_id": 25718,
"hgvs_c": "c.1016G>A",
"hgvs_p": "p.Arg339Gln",
"transcript": "ENST00000879554.1",
"protein_id": "ENSP00000549613.1",
"transcript_support_level": null,
"aa_start": 339,
"aa_end": null,
"aa_length": 501,
"cds_start": 1016,
"cds_end": null,
"cds_length": 1506,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879554.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LPCAT1",
"gene_hgnc_id": 25718,
"hgvs_c": "c.842G>A",
"hgvs_p": "p.Arg281Gln",
"transcript": "ENST00000968004.1",
"protein_id": "ENSP00000638063.1",
"transcript_support_level": null,
"aa_start": 281,
"aa_end": null,
"aa_length": 476,
"cds_start": 842,
"cds_end": null,
"cds_length": 1431,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000968004.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LPCAT1",
"gene_hgnc_id": 25718,
"hgvs_c": "c.1259G>A",
"hgvs_p": "p.Arg420Gln",
"transcript": "XM_011514132.2",
"protein_id": "XP_011512434.2",
"transcript_support_level": null,
"aa_start": 420,
"aa_end": null,
"aa_length": 615,
"cds_start": 1259,
"cds_end": null,
"cds_length": 1848,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011514132.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LPCAT1",
"gene_hgnc_id": 25718,
"hgvs_c": "c.893G>A",
"hgvs_p": "p.Arg298Gln",
"transcript": "XM_011514134.2",
"protein_id": "XP_011512436.1",
"transcript_support_level": null,
"aa_start": 298,
"aa_end": null,
"aa_length": 493,
"cds_start": 893,
"cds_end": null,
"cds_length": 1482,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011514134.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LPCAT1",
"gene_hgnc_id": 25718,
"hgvs_c": "c.872G>A",
"hgvs_p": "p.Arg291Gln",
"transcript": "XM_005248373.4",
"protein_id": "XP_005248430.1",
"transcript_support_level": null,
"aa_start": 291,
"aa_end": null,
"aa_length": 486,
"cds_start": 872,
"cds_end": null,
"cds_length": 1461,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005248373.4"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LPCAT1",
"gene_hgnc_id": 25718,
"hgvs_c": "c.872G>A",
"hgvs_p": "p.Arg291Gln",
"transcript": "XM_047417763.1",
"protein_id": "XP_047273719.1",
"transcript_support_level": null,
"aa_start": 291,
"aa_end": null,
"aa_length": 486,
"cds_start": 872,
"cds_end": null,
"cds_length": 1461,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417763.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "LPCAT1",
"gene_hgnc_id": 25718,
"hgvs_c": "c.900-459G>A",
"hgvs_p": null,
"transcript": "ENST00000968003.1",
"protein_id": "ENSP00000638062.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 492,
"cds_start": null,
"cds_end": null,
"cds_length": 1479,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000968003.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LPCAT1",
"gene_hgnc_id": 25718,
"hgvs_c": "n.1016G>A",
"hgvs_p": null,
"transcript": "ENST00000475622.6",
"protein_id": "ENSP00000423472.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000475622.6"
}
],
"gene_symbol": "LPCAT1",
"gene_hgnc_id": 25718,
"dbsnp": "rs1734820490",
"frequency_reference_population": 0.000004105214,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000410521,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6655187010765076,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.139,
"revel_prediction": "Benign",
"alphamissense_score": 0.1593,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.19,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.892,
"phylop100way_prediction": "Uncertain_significance",
"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": "NM_024830.5",
"gene_symbol": "LPCAT1",
"hgnc_id": 25718,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1016G>A",
"hgvs_p": "p.Arg339Gln"
}
],
"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
}