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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: 10-88678450-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=88678450&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 88678450,
"ref": "A",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "NM_001198829.2",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPF",
"gene_hgnc_id": 6622,
"hgvs_c": "c.966A>G",
"hgvs_p": "p.Gln322Gln",
"transcript": "NM_004190.4",
"protein_id": "NP_004181.1",
"transcript_support_level": null,
"aa_start": 322,
"aa_end": null,
"aa_length": 398,
"cds_start": 966,
"cds_end": null,
"cds_length": 1197,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000238983.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004190.4"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPF",
"gene_hgnc_id": 6622,
"hgvs_c": "c.966A>G",
"hgvs_p": "p.Gln322Gln",
"transcript": "ENST00000238983.9",
"protein_id": "ENSP00000238983.5",
"transcript_support_level": 1,
"aa_start": 322,
"aa_end": null,
"aa_length": 398,
"cds_start": 966,
"cds_end": null,
"cds_length": 1197,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004190.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000238983.9"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPF",
"gene_hgnc_id": 6622,
"hgvs_c": "c.897A>G",
"hgvs_p": "p.Gln299Gln",
"transcript": "ENST00000355843.2",
"protein_id": "ENSP00000348101.3",
"transcript_support_level": 1,
"aa_start": 299,
"aa_end": null,
"aa_length": 375,
"cds_start": 897,
"cds_end": null,
"cds_length": 1128,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000355843.2"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPF",
"gene_hgnc_id": 6622,
"hgvs_c": "c.996A>G",
"hgvs_p": "p.Gln332Gln",
"transcript": "NM_001198829.2",
"protein_id": "NP_001185758.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 408,
"cds_start": 996,
"cds_end": null,
"cds_length": 1227,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001198829.2"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPF",
"gene_hgnc_id": 6622,
"hgvs_c": "c.996A>G",
"hgvs_p": "p.Gln332Gln",
"transcript": "ENST00000394375.7",
"protein_id": "ENSP00000377900.3",
"transcript_support_level": 2,
"aa_start": 332,
"aa_end": null,
"aa_length": 408,
"cds_start": 996,
"cds_end": null,
"cds_length": 1227,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000394375.7"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPF",
"gene_hgnc_id": 6622,
"hgvs_c": "c.897A>G",
"hgvs_p": "p.Gln299Gln",
"transcript": "NM_001198830.2",
"protein_id": "NP_001185759.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 375,
"cds_start": 897,
"cds_end": null,
"cds_length": 1128,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001198830.2"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPF",
"gene_hgnc_id": 6622,
"hgvs_c": "c.867A>G",
"hgvs_p": "p.Gln289Gln",
"transcript": "NM_001198828.2",
"protein_id": "NP_001185757.1",
"transcript_support_level": null,
"aa_start": 289,
"aa_end": null,
"aa_length": 365,
"cds_start": 867,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001198828.2"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPF",
"gene_hgnc_id": 6622,
"hgvs_c": "c.867A>G",
"hgvs_p": "p.Gln289Gln",
"transcript": "ENST00000608620.5",
"protein_id": "ENSP00000477140.1",
"transcript_support_level": 2,
"aa_start": 289,
"aa_end": null,
"aa_length": 365,
"cds_start": 867,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000608620.5"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPF",
"gene_hgnc_id": 6622,
"hgvs_c": "c.966A>G",
"hgvs_p": "p.Gln322Gln",
"transcript": "XM_011540311.2",
"protein_id": "XP_011538613.1",
"transcript_support_level": null,
"aa_start": 322,
"aa_end": null,
"aa_length": 398,
"cds_start": 966,
"cds_end": null,
"cds_length": 1197,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011540311.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "LIPF",
"gene_hgnc_id": 6622,
"hgvs_c": "n.243A>G",
"hgvs_p": null,
"transcript": "ENST00000496797.1",
"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": "ENST00000496797.1"
}
],
"gene_symbol": "LIPF",
"gene_hgnc_id": 6622,
"dbsnp": "rs1228187",
"frequency_reference_population": 0.2075588,
"hom_count_reference_population": 35934,
"allele_count_reference_population": 334256,
"gnomad_exomes_af": 0.208585,
"gnomad_genomes_af": 0.19771,
"gnomad_exomes_ac": 304210,
"gnomad_genomes_ac": 30046,
"gnomad_exomes_homalt": 32806,
"gnomad_genomes_homalt": 3128,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8700000047683716,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.87,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.543,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_001198829.2",
"gene_symbol": "LIPF",
"hgnc_id": 6622,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.996A>G",
"hgvs_p": "p.Gln332Gln"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}