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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: 4-25234216-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=25234216&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 25234216,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_018323.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PI4K2B",
"gene_hgnc_id": 18215,
"hgvs_c": "c.53C>T",
"hgvs_p": "p.Pro18Leu",
"transcript": "NM_018323.4",
"protein_id": "NP_060793.2",
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 481,
"cds_start": 53,
"cds_end": null,
"cds_length": 1446,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000264864.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018323.4"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PI4K2B",
"gene_hgnc_id": 18215,
"hgvs_c": "c.53C>T",
"hgvs_p": "p.Pro18Leu",
"transcript": "ENST00000264864.8",
"protein_id": "ENSP00000264864.6",
"transcript_support_level": 1,
"aa_start": 18,
"aa_end": null,
"aa_length": 481,
"cds_start": 53,
"cds_end": null,
"cds_length": 1446,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_018323.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264864.8"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PI4K2B",
"gene_hgnc_id": 18215,
"hgvs_c": "c.53C>T",
"hgvs_p": "p.Pro18Leu",
"transcript": "ENST00000871538.1",
"protein_id": "ENSP00000541597.1",
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 481,
"cds_start": 53,
"cds_end": null,
"cds_length": 1446,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871538.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PI4K2B",
"gene_hgnc_id": 18215,
"hgvs_c": "c.53C>T",
"hgvs_p": "p.Pro18Leu",
"transcript": "ENST00000963199.1",
"protein_id": "ENSP00000633258.1",
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 476,
"cds_start": 53,
"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": "ENST00000963199.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PI4K2B",
"gene_hgnc_id": 18215,
"hgvs_c": "c.53C>T",
"hgvs_p": "p.Pro18Leu",
"transcript": "ENST00000963200.1",
"protein_id": "ENSP00000633259.1",
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 470,
"cds_start": 53,
"cds_end": null,
"cds_length": 1413,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963200.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PI4K2B",
"gene_hgnc_id": 18215,
"hgvs_c": "c.53C>T",
"hgvs_p": "p.Pro18Leu",
"transcript": "ENST00000871539.1",
"protein_id": "ENSP00000541598.1",
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 461,
"cds_start": 53,
"cds_end": null,
"cds_length": 1386,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871539.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PI4K2B",
"gene_hgnc_id": 18215,
"hgvs_c": "c.53C>T",
"hgvs_p": "p.Pro18Leu",
"transcript": "ENST00000871540.1",
"protein_id": "ENSP00000541599.1",
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 407,
"cds_start": 53,
"cds_end": null,
"cds_length": 1224,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871540.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PI4K2B",
"gene_hgnc_id": 18215,
"hgvs_c": "c.53C>T",
"hgvs_p": "p.Pro18Leu",
"transcript": "XM_005248174.3",
"protein_id": "XP_005248231.1",
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 476,
"cds_start": 53,
"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": "XM_005248174.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PI4K2B",
"gene_hgnc_id": 18215,
"hgvs_c": "c.-20-18105C>T",
"hgvs_p": null,
"transcript": "ENST00000512921.4",
"protein_id": "ENSP00000423373.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 385,
"cds_start": null,
"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": "ENST00000512921.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PI4K2B",
"gene_hgnc_id": 18215,
"hgvs_c": "n.184C>T",
"hgvs_p": null,
"transcript": "NR_144633.2",
"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_144633.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "PI4K2B",
"gene_hgnc_id": 18215,
"hgvs_c": "n.184C>T",
"hgvs_p": null,
"transcript": "XR_007057941.1",
"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": "XR_007057941.1"
}
],
"gene_symbol": "PI4K2B",
"gene_hgnc_id": 18215,
"dbsnp": "rs1057456837",
"frequency_reference_population": 0.0000042498214,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000238146,
"gnomad_genomes_af": 0.0000197249,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.05876043438911438,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.038,
"revel_prediction": "Benign",
"alphamissense_score": 0.0728,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.55,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.167,
"phylop100way_prediction": "Benign",
"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": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_018323.4",
"gene_symbol": "PI4K2B",
"hgnc_id": 18215,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.53C>T",
"hgvs_p": "p.Pro18Leu"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}