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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: 9-109457194-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=109457194&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 109457194,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000374541.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.268G>C",
"hgvs_p": "p.Ala90Pro",
"transcript": "NM_002829.4",
"protein_id": "NP_002820.3",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 913,
"cds_start": 268,
"cds_end": null,
"cds_length": 2742,
"cdna_start": 374,
"cdna_end": null,
"cdna_length": 6704,
"mane_select": "ENST00000374541.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.268G>C",
"hgvs_p": "p.Ala90Pro",
"transcript": "ENST00000374541.4",
"protein_id": "ENSP00000363667.1",
"transcript_support_level": 5,
"aa_start": 90,
"aa_end": null,
"aa_length": 913,
"cds_start": 268,
"cds_end": null,
"cds_length": 2742,
"cdna_start": 374,
"cdna_end": null,
"cdna_length": 6704,
"mane_select": "NM_002829.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.268G>C",
"hgvs_p": "p.Ala90Pro",
"transcript": "NM_001145368.2",
"protein_id": "NP_001138840.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 868,
"cds_start": 268,
"cds_end": null,
"cds_length": 2607,
"cdna_start": 374,
"cdna_end": null,
"cdna_length": 6569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.268G>C",
"hgvs_p": "p.Ala90Pro",
"transcript": "ENST00000262539.7",
"protein_id": "ENSP00000262539.4",
"transcript_support_level": 5,
"aa_start": 90,
"aa_end": null,
"aa_length": 839,
"cds_start": 268,
"cds_end": null,
"cds_length": 2520,
"cdna_start": 380,
"cdna_end": null,
"cdna_length": 6832,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.331G>C",
"hgvs_p": "p.Ala111Pro",
"transcript": "XM_011518888.3",
"protein_id": "XP_011517190.1",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 934,
"cds_start": 331,
"cds_end": null,
"cds_length": 2805,
"cdna_start": 475,
"cdna_end": null,
"cdna_length": 6805,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.448G>C",
"hgvs_p": "p.Ala150Pro",
"transcript": "XM_047423635.1",
"protein_id": "XP_047279591.1",
"transcript_support_level": null,
"aa_start": 150,
"aa_end": null,
"aa_length": 928,
"cds_start": 448,
"cds_end": null,
"cds_length": 2787,
"cdna_start": 552,
"cdna_end": null,
"cdna_length": 6747,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.301G>C",
"hgvs_p": "p.Ala101Pro",
"transcript": "XM_047423636.1",
"protein_id": "XP_047279592.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 924,
"cds_start": 301,
"cds_end": null,
"cds_length": 2775,
"cdna_start": 4310,
"cdna_end": null,
"cdna_length": 10640,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.268G>C",
"hgvs_p": "p.Ala90Pro",
"transcript": "XM_006717199.4",
"protein_id": "XP_006717262.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 913,
"cds_start": 268,
"cds_end": null,
"cds_length": 2742,
"cdna_start": 559,
"cdna_end": null,
"cdna_length": 6889,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.268G>C",
"hgvs_p": "p.Ala90Pro",
"transcript": "XM_017014955.2",
"protein_id": "XP_016870444.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 913,
"cds_start": 268,
"cds_end": null,
"cds_length": 2742,
"cdna_start": 5867,
"cdna_end": null,
"cdna_length": 12197,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.268G>C",
"hgvs_p": "p.Ala90Pro",
"transcript": "XM_047423634.1",
"protein_id": "XP_047279590.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 913,
"cds_start": 268,
"cds_end": null,
"cds_length": 2742,
"cdna_start": 346,
"cdna_end": null,
"cdna_length": 6676,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.301G>C",
"hgvs_p": "p.Ala101Pro",
"transcript": "XM_047423637.1",
"protein_id": "XP_047279593.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 879,
"cds_start": 301,
"cds_end": null,
"cds_length": 2640,
"cdna_start": 489,
"cdna_end": null,
"cdna_length": 6684,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"hgvs_c": "c.20G>C",
"hgvs_p": "p.Ser7Thr",
"transcript": "XM_047423638.1",
"protein_id": "XP_047279594.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 804,
"cds_start": 20,
"cds_end": null,
"cds_length": 2415,
"cdna_start": 79,
"cdna_end": null,
"cdna_length": 6330,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTPN3",
"gene_hgnc_id": 9655,
"dbsnp": "rs3793524",
"frequency_reference_population": 0.35328665,
"hom_count_reference_population": 103209,
"allele_count_reference_population": 569874,
"gnomad_exomes_af": 0.350711,
"gnomad_genomes_af": 0.378029,
"gnomad_exomes_ac": 512375,
"gnomad_genomes_ac": 57499,
"gnomad_exomes_homalt": 91779,
"gnomad_genomes_homalt": 11430,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0009142458438873291,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.354,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0472,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.45,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.935,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000374541.4",
"gene_symbol": "PTPN3",
"hgnc_id": 9655,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown",
"hgvs_c": "c.268G>C",
"hgvs_p": "p.Ala90Pro"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}