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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: 15-75470769-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=75470769&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 75470769,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_002833.4",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.1270A>G",
"hgvs_p": "p.Ile424Val",
"transcript": "NM_002833.4",
"protein_id": "NP_002824.1",
"transcript_support_level": null,
"aa_start": 424,
"aa_end": null,
"aa_length": 593,
"cds_start": 1270,
"cds_end": null,
"cds_length": 1782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000618819.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002833.4"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.1270A>G",
"hgvs_p": "p.Ile424Val",
"transcript": "ENST00000618819.5",
"protein_id": "ENSP00000482732.1",
"transcript_support_level": 1,
"aa_start": 424,
"aa_end": null,
"aa_length": 593,
"cds_start": 1270,
"cds_end": null,
"cds_length": 1782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002833.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000618819.5"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.1387A>G",
"hgvs_p": "p.Ile463Val",
"transcript": "ENST00000944252.1",
"protein_id": "ENSP00000614311.1",
"transcript_support_level": null,
"aa_start": 463,
"aa_end": null,
"aa_length": 632,
"cds_start": 1387,
"cds_end": null,
"cds_length": 1899,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944252.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.1318A>G",
"hgvs_p": "p.Ile440Val",
"transcript": "ENST00000893935.1",
"protein_id": "ENSP00000563994.1",
"transcript_support_level": null,
"aa_start": 440,
"aa_end": null,
"aa_length": 609,
"cds_start": 1318,
"cds_end": null,
"cds_length": 1830,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000893935.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.1309A>G",
"hgvs_p": "p.Ile437Val",
"transcript": "ENST00000893936.1",
"protein_id": "ENSP00000563995.1",
"transcript_support_level": null,
"aa_start": 437,
"aa_end": null,
"aa_length": 606,
"cds_start": 1309,
"cds_end": null,
"cds_length": 1821,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000893936.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.1219A>G",
"hgvs_p": "p.Ile407Val",
"transcript": "ENST00000893938.1",
"protein_id": "ENSP00000563997.1",
"transcript_support_level": null,
"aa_start": 407,
"aa_end": null,
"aa_length": 576,
"cds_start": 1219,
"cds_end": null,
"cds_length": 1731,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000893938.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.1180A>G",
"hgvs_p": "p.Ile394Val",
"transcript": "ENST00000936113.1",
"protein_id": "ENSP00000606172.1",
"transcript_support_level": null,
"aa_start": 394,
"aa_end": null,
"aa_length": 563,
"cds_start": 1180,
"cds_end": null,
"cds_length": 1692,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936113.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.1174A>G",
"hgvs_p": "p.Ile392Val",
"transcript": "ENST00000944253.1",
"protein_id": "ENSP00000614312.1",
"transcript_support_level": null,
"aa_start": 392,
"aa_end": null,
"aa_length": 561,
"cds_start": 1174,
"cds_end": null,
"cds_length": 1686,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944253.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.1165A>G",
"hgvs_p": "p.Ile389Val",
"transcript": "ENST00000936115.1",
"protein_id": "ENSP00000606174.1",
"transcript_support_level": null,
"aa_start": 389,
"aa_end": null,
"aa_length": 558,
"cds_start": 1165,
"cds_end": null,
"cds_length": 1677,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936115.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.1126A>G",
"hgvs_p": "p.Ile376Val",
"transcript": "ENST00000893934.1",
"protein_id": "ENSP00000563993.1",
"transcript_support_level": null,
"aa_start": 376,
"aa_end": null,
"aa_length": 545,
"cds_start": 1126,
"cds_end": null,
"cds_length": 1638,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000893934.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.1036A>G",
"hgvs_p": "p.Ile346Val",
"transcript": "ENST00000936114.1",
"protein_id": "ENSP00000606173.1",
"transcript_support_level": null,
"aa_start": 346,
"aa_end": null,
"aa_length": 515,
"cds_start": 1036,
"cds_end": null,
"cds_length": 1548,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936114.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.1012A>G",
"hgvs_p": "p.Ile338Val",
"transcript": "ENST00000893937.1",
"protein_id": "ENSP00000563996.1",
"transcript_support_level": null,
"aa_start": 338,
"aa_end": null,
"aa_length": 507,
"cds_start": 1012,
"cds_end": null,
"cds_length": 1524,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000893937.1"
},
{
"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": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "n.141A>G",
"hgvs_p": null,
"transcript": "ENST00000568108.1",
"protein_id": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000568108.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "LOC105370902",
"gene_hgnc_id": null,
"hgvs_c": "n.8T>C",
"hgvs_p": null,
"transcript": "XR_001751804.2",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_001751804.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC105370902",
"gene_hgnc_id": null,
"hgvs_c": "n.8T>C",
"hgvs_p": null,
"transcript": "XR_932482.2",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_932482.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "LOC105370902",
"gene_hgnc_id": null,
"hgvs_c": "n.8T>C",
"hgvs_p": null,
"transcript": "XR_932483.2",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_932483.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "n.149-770A>G",
"hgvs_p": null,
"transcript": "ENST00000563835.1",
"protein_id": null,
"transcript_support_level": 5,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000563835.1"
}
],
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"dbsnp": "rs138474126",
"frequency_reference_population": 0.000005575393,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000342023,
"gnomad_genomes_af": 0.0000262564,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.030164778232574463,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.054,
"revel_prediction": "Benign",
"alphamissense_score": 0.0707,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.73,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.618,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_002833.4",
"gene_symbol": "PTPN9",
"hgnc_id": 9661,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1270A>G",
"hgvs_p": "p.Ile424Val"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "XR_932482.2",
"gene_symbol": "LOC105370902",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.8T>C",
"hgvs_p": null
}
],
"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
}