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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: 20-9539494-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=9539494&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 9539494,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_020341.5",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK5",
"gene_hgnc_id": 15916,
"hgvs_c": "c.2128G>A",
"hgvs_p": "p.Val710Ile",
"transcript": "NM_177990.4",
"protein_id": "NP_817127.1",
"transcript_support_level": null,
"aa_start": 710,
"aa_end": null,
"aa_length": 719,
"cds_start": 2128,
"cds_end": null,
"cds_length": 2160,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000353224.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_177990.4"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK5",
"gene_hgnc_id": 15916,
"hgvs_c": "c.2128G>A",
"hgvs_p": "p.Val710Ile",
"transcript": "ENST00000353224.10",
"protein_id": "ENSP00000322957.5",
"transcript_support_level": 1,
"aa_start": 710,
"aa_end": null,
"aa_length": 719,
"cds_start": 2128,
"cds_end": null,
"cds_length": 2160,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_177990.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000353224.10"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK5",
"gene_hgnc_id": 15916,
"hgvs_c": "c.2128G>A",
"hgvs_p": "p.Val710Ile",
"transcript": "ENST00000378423.5",
"protein_id": "ENSP00000367679.1",
"transcript_support_level": 1,
"aa_start": 710,
"aa_end": null,
"aa_length": 719,
"cds_start": 2128,
"cds_end": null,
"cds_length": 2160,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000378423.5"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK5",
"gene_hgnc_id": 15916,
"hgvs_c": "c.2128G>A",
"hgvs_p": "p.Val710Ile",
"transcript": "ENST00000378429.3",
"protein_id": "ENSP00000367686.3",
"transcript_support_level": 1,
"aa_start": 710,
"aa_end": null,
"aa_length": 719,
"cds_start": 2128,
"cds_end": null,
"cds_length": 2160,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000378429.3"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK5",
"gene_hgnc_id": 15916,
"hgvs_c": "c.2128G>A",
"hgvs_p": "p.Val710Ile",
"transcript": "NM_020341.5",
"protein_id": "NP_065074.1",
"transcript_support_level": null,
"aa_start": 710,
"aa_end": null,
"aa_length": 719,
"cds_start": 2128,
"cds_end": null,
"cds_length": 2160,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_020341.5"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK5",
"gene_hgnc_id": 15916,
"hgvs_c": "c.1636G>A",
"hgvs_p": "p.Val546Ile",
"transcript": "ENST00000875443.1",
"protein_id": "ENSP00000545502.1",
"transcript_support_level": null,
"aa_start": 546,
"aa_end": null,
"aa_length": 555,
"cds_start": 1636,
"cds_end": null,
"cds_length": 1668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875443.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK5",
"gene_hgnc_id": 15916,
"hgvs_c": "c.1342G>A",
"hgvs_p": "p.Val448Ile",
"transcript": "ENST00000959437.1",
"protein_id": "ENSP00000629496.1",
"transcript_support_level": null,
"aa_start": 448,
"aa_end": null,
"aa_length": 457,
"cds_start": 1342,
"cds_end": null,
"cds_length": 1374,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000959437.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK5",
"gene_hgnc_id": 15916,
"hgvs_c": "c.2128G>A",
"hgvs_p": "p.Val710Ile",
"transcript": "XM_017027960.2",
"protein_id": "XP_016883449.1",
"transcript_support_level": null,
"aa_start": 710,
"aa_end": null,
"aa_length": 719,
"cds_start": 2128,
"cds_end": null,
"cds_length": 2160,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017027960.2"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK5",
"gene_hgnc_id": 15916,
"hgvs_c": "c.2128G>A",
"hgvs_p": "p.Val710Ile",
"transcript": "XM_017027961.2",
"protein_id": "XP_016883450.1",
"transcript_support_level": null,
"aa_start": 710,
"aa_end": null,
"aa_length": 719,
"cds_start": 2128,
"cds_end": null,
"cds_length": 2160,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017027961.2"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK5",
"gene_hgnc_id": 15916,
"hgvs_c": "c.2128G>A",
"hgvs_p": "p.Val710Ile",
"transcript": "XM_017027962.2",
"protein_id": "XP_016883451.1",
"transcript_support_level": null,
"aa_start": 710,
"aa_end": null,
"aa_length": 719,
"cds_start": 2128,
"cds_end": null,
"cds_length": 2160,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017027962.2"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK5",
"gene_hgnc_id": 15916,
"hgvs_c": "c.2128G>A",
"hgvs_p": "p.Val710Ile",
"transcript": "XM_017027964.2",
"protein_id": "XP_016883453.1",
"transcript_support_level": null,
"aa_start": 710,
"aa_end": null,
"aa_length": 719,
"cds_start": 2128,
"cds_end": null,
"cds_length": 2160,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017027964.2"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAK5",
"gene_hgnc_id": 15916,
"hgvs_c": "c.2128G>A",
"hgvs_p": "p.Val710Ile",
"transcript": "XM_017027965.2",
"protein_id": "XP_016883454.1",
"transcript_support_level": null,
"aa_start": 710,
"aa_end": null,
"aa_length": 719,
"cds_start": 2128,
"cds_end": null,
"cds_length": 2160,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017027965.2"
}
],
"gene_symbol": "PAK5",
"gene_hgnc_id": 15916,
"dbsnp": "rs560752200",
"frequency_reference_population": 0.000018587843,
"hom_count_reference_population": 1,
"allele_count_reference_population": 30,
"gnomad_exomes_af": 0.0000171031,
"gnomad_genomes_af": 0.0000328446,
"gnomad_exomes_ac": 25,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1565343737602234,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.13,
"revel_prediction": "Benign",
"alphamissense_score": 0.0809,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.32,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.171,
"phylop100way_prediction": "Uncertain_significance",
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_020341.5",
"gene_symbol": "PAK5",
"hgnc_id": 15916,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2128G>A",
"hgvs_p": "p.Val710Ile"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}