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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: 19-39423713-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=39423713&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 39423713,
"ref": "G",
"alt": "A",
"effect": "intron_variant",
"transcript": "NM_022835.3",
"consequences": [
{
"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": 19,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "PLEKHG2",
"gene_hgnc_id": 29515,
"hgvs_c": "c.2600-20G>A",
"hgvs_p": null,
"transcript": "NM_022835.3",
"protein_id": "NP_073746.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1386,
"cds_start": null,
"cds_end": null,
"cds_length": 4161,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000425673.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_022835.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "PLEKHG2",
"gene_hgnc_id": 29515,
"hgvs_c": "c.2600-20G>A",
"hgvs_p": null,
"transcript": "ENST00000425673.6",
"protein_id": "ENSP00000392906.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 1386,
"cds_start": null,
"cds_end": null,
"cds_length": 4161,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_022835.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000425673.6"
},
{
"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": 15,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "PLEKHG2",
"gene_hgnc_id": 29515,
"hgvs_c": "c.2201-20G>A",
"hgvs_p": null,
"transcript": "ENST00000205135.8",
"protein_id": "ENSP00000205135.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1253,
"cds_start": null,
"cds_end": null,
"cds_length": 3762,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000205135.8"
},
{
"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": 18,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "PLEKHG2",
"gene_hgnc_id": 29515,
"hgvs_c": "c.2600-20G>A",
"hgvs_p": null,
"transcript": "ENST00000942561.1",
"protein_id": "ENSP00000612620.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1386,
"cds_start": null,
"cds_end": null,
"cds_length": 4161,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942561.1"
},
{
"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": 19,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "PLEKHG2",
"gene_hgnc_id": 29515,
"hgvs_c": "c.2600-20G>A",
"hgvs_p": null,
"transcript": "ENST00000942562.1",
"protein_id": "ENSP00000612621.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1386,
"cds_start": null,
"cds_end": null,
"cds_length": 4161,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942562.1"
},
{
"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": 20,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "PLEKHG2",
"gene_hgnc_id": 29515,
"hgvs_c": "c.2423-20G>A",
"hgvs_p": null,
"transcript": "NM_001351693.2",
"protein_id": "NP_001338622.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1237,
"cds_start": null,
"cds_end": null,
"cds_length": 3714,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001351693.2"
},
{
"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": 20,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "PLEKHG2",
"gene_hgnc_id": 29515,
"hgvs_c": "c.2423-20G>A",
"hgvs_p": null,
"transcript": "ENST00000458508.6",
"protein_id": "ENSP00000408857.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 1237,
"cds_start": null,
"cds_end": null,
"cds_length": 3714,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000458508.6"
},
{
"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": 18,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "PLEKHG2",
"gene_hgnc_id": 29515,
"hgvs_c": "c.1677+1425G>A",
"hgvs_p": null,
"transcript": "NM_001351694.2",
"protein_id": "NP_001338623.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 577,
"cds_start": null,
"cds_end": null,
"cds_length": 1734,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001351694.2"
},
{
"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": 18,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "PLEKHG2",
"gene_hgnc_id": 29515,
"hgvs_c": "c.1677+1425G>A",
"hgvs_p": null,
"transcript": "ENST00000409797.6",
"protein_id": "ENSP00000386492.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 577,
"cds_start": null,
"cds_end": null,
"cds_length": 1734,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409797.6"
},
{
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PLEKHG2",
"gene_hgnc_id": 29515,
"hgvs_c": "c.291+1425G>A",
"hgvs_p": null,
"transcript": "ENST00000596443.1",
"protein_id": "ENSP00000468829.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 115,
"cds_start": null,
"cds_end": null,
"cds_length": 348,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000596443.1"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PLEKHG2",
"gene_hgnc_id": 29515,
"hgvs_c": "c.227-20G>A",
"hgvs_p": null,
"transcript": "ENST00000600210.1",
"protein_id": "ENSP00000473251.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 103,
"cds_start": null,
"cds_end": null,
"cds_length": 312,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000600210.1"
}
],
"gene_symbol": "PLEKHG2",
"gene_hgnc_id": 29515,
"dbsnp": "rs73930732",
"frequency_reference_population": 0.0027380302,
"hom_count_reference_population": 89,
"allele_count_reference_population": 4375,
"gnomad_exomes_af": 0.00154609,
"gnomad_genomes_af": 0.0140525,
"gnomad_exomes_ac": 2235,
"gnomad_genomes_ac": 2140,
"gnomad_exomes_homalt": 48,
"gnomad_genomes_homalt": 41,
"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,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.97,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -4.657,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_022835.3",
"gene_symbol": "PLEKHG2",
"hgnc_id": 29515,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.2600-20G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}