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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: 3-52819385-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=52819385&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 52819385,
"ref": "C",
"alt": "T",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000266041.9",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000243696",
"gene_hgnc_id": null,
"hgvs_c": "n.*2599G>A",
"hgvs_p": null,
"transcript": "ENST00000468472.1",
"protein_id": "ENSP00000422253.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5640,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000243696",
"gene_hgnc_id": null,
"hgvs_c": "n.*2599G>A",
"hgvs_p": null,
"transcript": "ENST00000468472.1",
"protein_id": "ENSP00000422253.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5640,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "ITIH4",
"gene_hgnc_id": 6169,
"hgvs_c": "c.2077+8G>A",
"hgvs_p": null,
"transcript": "NM_002218.5",
"protein_id": "NP_002209.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 930,
"cds_start": -4,
"cds_end": null,
"cds_length": 2793,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3282,
"mane_select": "ENST00000266041.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "ITIH4",
"gene_hgnc_id": 6169,
"hgvs_c": "c.2077+8G>A",
"hgvs_p": null,
"transcript": "ENST00000266041.9",
"protein_id": "ENSP00000266041.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 930,
"cds_start": -4,
"cds_end": null,
"cds_length": 2793,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3282,
"mane_select": "NM_002218.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "ITIH4",
"gene_hgnc_id": 6169,
"hgvs_c": "c.2092+8G>A",
"hgvs_p": null,
"transcript": "ENST00000485816.5",
"protein_id": "ENSP00000417824.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 935,
"cds_start": -4,
"cds_end": null,
"cds_length": 2808,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2990,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ITIH4",
"gene_hgnc_id": 6169,
"hgvs_c": "c.1558+8G>A",
"hgvs_p": null,
"transcript": "ENST00000441637.2",
"protein_id": "ENSP00000395634.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 718,
"cds_start": -4,
"cds_end": null,
"cds_length": 2157,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2293,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "ITIH4",
"gene_hgnc_id": 6169,
"hgvs_c": "c.1987+8G>A",
"hgvs_p": null,
"transcript": "NM_001166449.2",
"protein_id": "NP_001159921.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 900,
"cds_start": -4,
"cds_end": null,
"cds_length": 2703,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3192,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "ITIH4",
"gene_hgnc_id": 6169,
"hgvs_c": "c.1987+8G>A",
"hgvs_p": null,
"transcript": "ENST00000406595.5",
"protein_id": "ENSP00000384425.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 900,
"cds_start": -4,
"cds_end": null,
"cds_length": 2703,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2872,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ITIH4",
"gene_hgnc_id": 6169,
"hgvs_c": "n.206+8G>A",
"hgvs_p": null,
"transcript": "ENST00000461966.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 775,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ITIH4",
"gene_hgnc_id": 6169,
"hgvs_c": "n.274+8G>A",
"hgvs_p": null,
"transcript": "ENST00000481977.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "ITIH4",
"gene_hgnc_id": 6169,
"hgvs_c": "n.2269+8G>A",
"hgvs_p": null,
"transcript": "ENST00000491663.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3093,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "ITIH4",
"gene_hgnc_id": 6169,
"hgvs_c": "n.2109+8G>A",
"hgvs_p": null,
"transcript": "ENST00000537897.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2120,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ITIH4",
"gene_hgnc_id": 6169,
"dbsnp": "rs3821831",
"frequency_reference_population": 0.3433622,
"hom_count_reference_population": 100256,
"allele_count_reference_population": 553960,
"gnomad_exomes_af": 0.34908,
"gnomad_genomes_af": 0.28845,
"gnomad_exomes_ac": 510070,
"gnomad_genomes_ac": 43890,
"gnomad_exomes_homalt": 93234,
"gnomad_genomes_homalt": 7022,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9700000286102295,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.01600000075995922,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.97,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.859,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000738514129904163,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BA1",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000266041.9",
"gene_symbol": "ITIH4",
"hgnc_id": 6169,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2077+8G>A",
"hgvs_p": null
},
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000468472.1",
"gene_symbol": "ENSG00000243696",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*2599G>A",
"hgvs_p": null
}
],
"clinvar_disease": " susceptibility to,Hypercholesterolemia",
"clinvar_classification": "Benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Hypercholesterolemia, susceptibility to",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}