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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: 14-88550324-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=88550324&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 88550324,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000556564.6",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.94A>C",
"hgvs_p": "p.Asn32His",
"transcript": "NM_007039.4",
"protein_id": "NP_008970.2",
"transcript_support_level": null,
"aa_start": 32,
"aa_end": null,
"aa_length": 1174,
"cds_start": 94,
"cds_end": null,
"cds_length": 3525,
"cdna_start": 653,
"cdna_end": null,
"cdna_length": 6443,
"mane_select": "ENST00000556564.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.94A>C",
"hgvs_p": "p.Asn32His",
"transcript": "ENST00000556564.6",
"protein_id": "ENSP00000452414.1",
"transcript_support_level": 1,
"aa_start": 32,
"aa_end": null,
"aa_length": 1174,
"cds_start": 94,
"cds_end": null,
"cds_length": 3525,
"cdna_start": 653,
"cdna_end": null,
"cdna_length": 6443,
"mane_select": "NM_007039.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.94A>C",
"hgvs_p": "p.Asn32His",
"transcript": "ENST00000328736.7",
"protein_id": "ENSP00000330276.3",
"transcript_support_level": 1,
"aa_start": 32,
"aa_end": null,
"aa_length": 1174,
"cds_start": 94,
"cds_end": null,
"cds_length": 3525,
"cdna_start": 299,
"cdna_end": null,
"cdna_length": 6089,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "n.94A>C",
"hgvs_p": null,
"transcript": "ENST00000536337.5",
"protein_id": "ENSP00000443951.1",
"transcript_support_level": 1,
"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": 3943,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "n.207A>C",
"hgvs_p": null,
"transcript": "ENST00000554270.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 4008,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "n.474A>C",
"hgvs_p": null,
"transcript": "ENST00000554628.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 1571,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.94A>C",
"hgvs_p": "p.Asn32His",
"transcript": "ENST00000555243.1",
"protein_id": "ENSP00000451401.1",
"transcript_support_level": 5,
"aa_start": 32,
"aa_end": null,
"aa_length": 194,
"cds_start": 94,
"cds_end": null,
"cds_length": 587,
"cdna_start": 521,
"cdna_end": null,
"cdna_length": 1014,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.94A>C",
"hgvs_p": "p.Asn32His",
"transcript": "XM_005267287.4",
"protein_id": "XP_005267344.1",
"transcript_support_level": null,
"aa_start": 32,
"aa_end": null,
"aa_length": 1174,
"cds_start": 94,
"cds_end": null,
"cds_length": 3525,
"cdna_start": 537,
"cdna_end": null,
"cdna_length": 6327,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.94A>C",
"hgvs_p": "p.Asn32His",
"transcript": "XM_011536367.4",
"protein_id": "XP_011534669.1",
"transcript_support_level": null,
"aa_start": 32,
"aa_end": null,
"aa_length": 1174,
"cds_start": 94,
"cds_end": null,
"cds_length": 3525,
"cdna_start": 613,
"cdna_end": null,
"cdna_length": 6403,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "n.296A>C",
"hgvs_p": null,
"transcript": "ENST00000554178.1",
"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": 822,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"dbsnp": "rs193920899",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.36568036675453186,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.334,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1075,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.27,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.117,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000556564.6",
"gene_symbol": "PTPN21",
"hgnc_id": 9651,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.94A>C",
"hgvs_p": "p.Asn32His"
}
],
"clinvar_disease": "Prostate cancer",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Prostate cancer",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}