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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: 3-47411889-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=47411889&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 47411889,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_015466.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN23",
"gene_hgnc_id": 14406,
"hgvs_c": "c.3995G>A",
"hgvs_p": "p.Arg1332His",
"transcript": "NM_015466.4",
"protein_id": "NP_056281.1",
"transcript_support_level": null,
"aa_start": 1332,
"aa_end": null,
"aa_length": 1636,
"cds_start": 3995,
"cds_end": null,
"cds_length": 4911,
"cdna_start": 4071,
"cdna_end": null,
"cdna_length": 5237,
"mane_select": "ENST00000265562.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015466.4"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN23",
"gene_hgnc_id": 14406,
"hgvs_c": "c.3995G>A",
"hgvs_p": "p.Arg1332His",
"transcript": "ENST00000265562.5",
"protein_id": "ENSP00000265562.4",
"transcript_support_level": 1,
"aa_start": 1332,
"aa_end": null,
"aa_length": 1636,
"cds_start": 3995,
"cds_end": null,
"cds_length": 4911,
"cdna_start": 4071,
"cdna_end": null,
"cdna_length": 5237,
"mane_select": "NM_015466.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000265562.5"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN23",
"gene_hgnc_id": 14406,
"hgvs_c": "c.4022G>A",
"hgvs_p": "p.Arg1341His",
"transcript": "ENST00000889694.1",
"protein_id": "ENSP00000559753.1",
"transcript_support_level": null,
"aa_start": 1341,
"aa_end": null,
"aa_length": 1645,
"cds_start": 4022,
"cds_end": null,
"cds_length": 4938,
"cdna_start": 4080,
"cdna_end": null,
"cdna_length": 5244,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889694.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN23",
"gene_hgnc_id": 14406,
"hgvs_c": "c.4004G>A",
"hgvs_p": "p.Arg1335His",
"transcript": "ENST00000918778.1",
"protein_id": "ENSP00000588837.1",
"transcript_support_level": null,
"aa_start": 1335,
"aa_end": null,
"aa_length": 1639,
"cds_start": 4004,
"cds_end": null,
"cds_length": 4920,
"cdna_start": 4076,
"cdna_end": null,
"cdna_length": 5242,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918778.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN23",
"gene_hgnc_id": 14406,
"hgvs_c": "c.3989G>A",
"hgvs_p": "p.Arg1330His",
"transcript": "ENST00000889696.1",
"protein_id": "ENSP00000559755.1",
"transcript_support_level": null,
"aa_start": 1330,
"aa_end": null,
"aa_length": 1634,
"cds_start": 3989,
"cds_end": null,
"cds_length": 4905,
"cdna_start": 4023,
"cdna_end": null,
"cdna_length": 5188,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889696.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN23",
"gene_hgnc_id": 14406,
"hgvs_c": "c.3965G>A",
"hgvs_p": "p.Arg1322His",
"transcript": "ENST00000889692.1",
"protein_id": "ENSP00000559751.1",
"transcript_support_level": null,
"aa_start": 1322,
"aa_end": null,
"aa_length": 1626,
"cds_start": 3965,
"cds_end": null,
"cds_length": 4881,
"cdna_start": 4051,
"cdna_end": null,
"cdna_length": 5223,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889692.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN23",
"gene_hgnc_id": 14406,
"hgvs_c": "c.3920G>A",
"hgvs_p": "p.Arg1307His",
"transcript": "ENST00000889693.1",
"protein_id": "ENSP00000559752.1",
"transcript_support_level": null,
"aa_start": 1307,
"aa_end": null,
"aa_length": 1611,
"cds_start": 3920,
"cds_end": null,
"cds_length": 4836,
"cdna_start": 3984,
"cdna_end": null,
"cdna_length": 5157,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889693.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN23",
"gene_hgnc_id": 14406,
"hgvs_c": "c.3740G>A",
"hgvs_p": "p.Arg1247His",
"transcript": "ENST00000889695.1",
"protein_id": "ENSP00000559754.1",
"transcript_support_level": null,
"aa_start": 1247,
"aa_end": null,
"aa_length": 1551,
"cds_start": 3740,
"cds_end": null,
"cds_length": 4656,
"cdna_start": 3784,
"cdna_end": null,
"cdna_length": 4951,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889695.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN23",
"gene_hgnc_id": 14406,
"hgvs_c": "c.3617G>A",
"hgvs_p": "p.Arg1206His",
"transcript": "NM_001304482.2",
"protein_id": "NP_001291411.1",
"transcript_support_level": null,
"aa_start": 1206,
"aa_end": null,
"aa_length": 1510,
"cds_start": 3617,
"cds_end": null,
"cds_length": 4533,
"cdna_start": 3943,
"cdna_end": null,
"cdna_length": 5109,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001304482.2"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN23",
"gene_hgnc_id": 14406,
"hgvs_c": "c.3965G>A",
"hgvs_p": "p.Arg1322His",
"transcript": "XM_005265031.3",
"protein_id": "XP_005265088.2",
"transcript_support_level": null,
"aa_start": 1322,
"aa_end": null,
"aa_length": 1626,
"cds_start": 3965,
"cds_end": null,
"cds_length": 4881,
"cdna_start": 4041,
"cdna_end": null,
"cdna_length": 5207,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005265031.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "PTPN23",
"gene_hgnc_id": 14406,
"hgvs_c": "n.*3672G>A",
"hgvs_p": null,
"transcript": "ENST00000602307.5",
"protein_id": "ENSP00000473266.1",
"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": 5119,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000602307.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN23",
"gene_hgnc_id": 14406,
"hgvs_c": "n.755G>A",
"hgvs_p": null,
"transcript": "ENST00000683708.1",
"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": 1364,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000683708.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN23",
"gene_hgnc_id": 14406,
"hgvs_c": "n.*3672G>A",
"hgvs_p": null,
"transcript": "ENST00000602307.5",
"protein_id": "ENSP00000473266.1",
"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": 5119,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000602307.5"
}
],
"gene_symbol": "PTPN23",
"gene_hgnc_id": 14406,
"dbsnp": "rs730882229",
"frequency_reference_population": 0.0000142577655,
"hom_count_reference_population": 0,
"allele_count_reference_population": 23,
"gnomad_exomes_af": 0.0000143721,
"gnomad_genomes_af": 0.0000131584,
"gnomad_exomes_ac": 21,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9702067971229553,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.54,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3512,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.09,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.181,
"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": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Strong",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PM5",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_015466.4",
"gene_symbol": "PTPN23",
"hgnc_id": 14406,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3995G>A",
"hgvs_p": "p.Arg1332His"
}
],
"clinvar_disease": "Neurodevelopmental disorder and structural brain anomalies with or without seizures and spasticity",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Neurodevelopmental disorder and structural brain anomalies with or without seizures and spasticity",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}