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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: 4-3532213-TG-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=3532213&ref=TG&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 3532213,
"ref": "TG",
"alt": "T",
"effect": "frameshift_variant",
"transcript": "NM_002337.4",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRPAP1",
"gene_hgnc_id": 6701,
"hgvs_c": "c.199delC",
"hgvs_p": "p.Gln67fs",
"transcript": "NM_002337.4",
"protein_id": "NP_002328.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 357,
"cds_start": 199,
"cds_end": null,
"cds_length": 1074,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000650182.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002337.4"
},
{
"aa_ref": "Q",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRPAP1",
"gene_hgnc_id": 6701,
"hgvs_c": "c.199delC",
"hgvs_p": "p.Gln67fs",
"transcript": "ENST00000650182.1",
"protein_id": "ENSP00000497444.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 357,
"cds_start": 199,
"cds_end": null,
"cds_length": 1074,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002337.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000650182.1"
},
{
"aa_ref": "Q",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRPAP1",
"gene_hgnc_id": 6701,
"hgvs_c": "c.199delC",
"hgvs_p": "p.Gln67fs",
"transcript": "ENST00000931150.1",
"protein_id": "ENSP00000601209.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 397,
"cds_start": 199,
"cds_end": null,
"cds_length": 1194,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931150.1"
},
{
"aa_ref": "Q",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRPAP1",
"gene_hgnc_id": 6701,
"hgvs_c": "c.199delC",
"hgvs_p": "p.Gln67fs",
"transcript": "ENST00000897675.1",
"protein_id": "ENSP00000567734.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 394,
"cds_start": 199,
"cds_end": null,
"cds_length": 1185,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000897675.1"
},
{
"aa_ref": "Q",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRPAP1",
"gene_hgnc_id": 6701,
"hgvs_c": "c.199delC",
"hgvs_p": "p.Gln67fs",
"transcript": "ENST00000897674.1",
"protein_id": "ENSP00000567733.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 385,
"cds_start": 199,
"cds_end": null,
"cds_length": 1158,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000897674.1"
},
{
"aa_ref": "Q",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRPAP1",
"gene_hgnc_id": 6701,
"hgvs_c": "c.199delC",
"hgvs_p": "p.Gln67fs",
"transcript": "ENST00000941405.1",
"protein_id": "ENSP00000611464.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 365,
"cds_start": 199,
"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": "ENST00000941405.1"
},
{
"aa_ref": "Q",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRPAP1",
"gene_hgnc_id": 6701,
"hgvs_c": "c.199delC",
"hgvs_p": "p.Gln67fs",
"transcript": "ENST00000897673.1",
"protein_id": "ENSP00000567732.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 356,
"cds_start": 199,
"cds_end": null,
"cds_length": 1071,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000897673.1"
},
{
"aa_ref": "Q",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRPAP1",
"gene_hgnc_id": 6701,
"hgvs_c": "c.199delC",
"hgvs_p": "p.Gln67fs",
"transcript": "ENST00000897672.1",
"protein_id": "ENSP00000567731.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 355,
"cds_start": 199,
"cds_end": null,
"cds_length": 1068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000897672.1"
},
{
"aa_ref": "Q",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRPAP1",
"gene_hgnc_id": 6701,
"hgvs_c": "c.199delC",
"hgvs_p": "p.Gln67fs",
"transcript": "ENST00000931149.1",
"protein_id": "ENSP00000601208.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 304,
"cds_start": 199,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931149.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRPAP1",
"gene_hgnc_id": 6701,
"hgvs_c": "n.209delC",
"hgvs_p": null,
"transcript": "ENST00000509198.1",
"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": "ENST00000509198.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRPAP1",
"gene_hgnc_id": 6701,
"hgvs_c": "n.199delC",
"hgvs_p": null,
"transcript": "ENST00000515119.5",
"protein_id": "ENSP00000421648.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000515119.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRPAP1",
"gene_hgnc_id": 6701,
"hgvs_c": "n.199delC",
"hgvs_p": null,
"transcript": "ENST00000648517.1",
"protein_id": "ENSP00000496947.1",
"transcript_support_level": null,
"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": "ENST00000648517.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRPAP1",
"gene_hgnc_id": 6701,
"hgvs_c": "n.233delC",
"hgvs_p": null,
"transcript": "ENST00000650633.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000650633.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRPAP1",
"gene_hgnc_id": 6701,
"hgvs_c": "n.-65delC",
"hgvs_p": null,
"transcript": "ENST00000296325.9",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000296325.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRPAP1",
"gene_hgnc_id": 6701,
"hgvs_c": "n.-65delC",
"hgvs_p": null,
"transcript": "NR_110005.2",
"protein_id": null,
"transcript_support_level": null,
"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": "NR_110005.2"
}
],
"gene_symbol": "LRPAP1",
"gene_hgnc_id": 6701,
"dbsnp": "rs786205216",
"frequency_reference_population": 0.000001430824,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000143082,
"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": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 1.572,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.07,
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "NM_002337.4",
"gene_symbol": "LRPAP1",
"hgnc_id": 6701,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.199delC",
"hgvs_p": "p.Gln67fs"
}
],
"clinvar_disease": " autosomal recessive,Myopia 23",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Myopia 23, autosomal recessive",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}