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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: 15-75473747-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=75473747&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 75473747,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_002833.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.1150C>T",
"hgvs_p": "p.Arg384Cys",
"transcript": "NM_002833.4",
"protein_id": "NP_002824.1",
"transcript_support_level": null,
"aa_start": 384,
"aa_end": null,
"aa_length": 593,
"cds_start": 1150,
"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": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.1150C>T",
"hgvs_p": "p.Arg384Cys",
"transcript": "ENST00000618819.5",
"protein_id": "ENSP00000482732.1",
"transcript_support_level": 1,
"aa_start": 384,
"aa_end": null,
"aa_length": 593,
"cds_start": 1150,
"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": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.1267C>T",
"hgvs_p": "p.Arg423Cys",
"transcript": "ENST00000944252.1",
"protein_id": "ENSP00000614311.1",
"transcript_support_level": null,
"aa_start": 423,
"aa_end": null,
"aa_length": 632,
"cds_start": 1267,
"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": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.1198C>T",
"hgvs_p": "p.Arg400Cys",
"transcript": "ENST00000893935.1",
"protein_id": "ENSP00000563994.1",
"transcript_support_level": null,
"aa_start": 400,
"aa_end": null,
"aa_length": 609,
"cds_start": 1198,
"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": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.1189C>T",
"hgvs_p": "p.Arg397Cys",
"transcript": "ENST00000893936.1",
"protein_id": "ENSP00000563995.1",
"transcript_support_level": null,
"aa_start": 397,
"aa_end": null,
"aa_length": 606,
"cds_start": 1189,
"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": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.1099C>T",
"hgvs_p": "p.Arg367Cys",
"transcript": "ENST00000893938.1",
"protein_id": "ENSP00000563997.1",
"transcript_support_level": null,
"aa_start": 367,
"aa_end": null,
"aa_length": 576,
"cds_start": 1099,
"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": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.1060C>T",
"hgvs_p": "p.Arg354Cys",
"transcript": "ENST00000936113.1",
"protein_id": "ENSP00000606172.1",
"transcript_support_level": null,
"aa_start": 354,
"aa_end": null,
"aa_length": 563,
"cds_start": 1060,
"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": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.1054C>T",
"hgvs_p": "p.Arg352Cys",
"transcript": "ENST00000944253.1",
"protein_id": "ENSP00000614312.1",
"transcript_support_level": null,
"aa_start": 352,
"aa_end": null,
"aa_length": 561,
"cds_start": 1054,
"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": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.1045C>T",
"hgvs_p": "p.Arg349Cys",
"transcript": "ENST00000936115.1",
"protein_id": "ENSP00000606174.1",
"transcript_support_level": null,
"aa_start": 349,
"aa_end": null,
"aa_length": 558,
"cds_start": 1045,
"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": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.1006C>T",
"hgvs_p": "p.Arg336Cys",
"transcript": "ENST00000893934.1",
"protein_id": "ENSP00000563993.1",
"transcript_support_level": null,
"aa_start": 336,
"aa_end": null,
"aa_length": 545,
"cds_start": 1006,
"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": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.916C>T",
"hgvs_p": "p.Arg306Cys",
"transcript": "ENST00000936114.1",
"protein_id": "ENSP00000606173.1",
"transcript_support_level": null,
"aa_start": 306,
"aa_end": null,
"aa_length": 515,
"cds_start": 916,
"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": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "c.892C>T",
"hgvs_p": "p.Arg298Cys",
"transcript": "ENST00000893937.1",
"protein_id": "ENSP00000563996.1",
"transcript_support_level": null,
"aa_start": 298,
"aa_end": null,
"aa_length": 507,
"cds_start": 892,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"hgvs_c": "n.90C>T",
"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"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC105370902",
"gene_hgnc_id": null,
"hgvs_c": "n.90-81G>A",
"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": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC105370902",
"gene_hgnc_id": null,
"hgvs_c": "n.90-81G>A",
"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": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC105370902",
"gene_hgnc_id": null,
"hgvs_c": "n.90-81G>A",
"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"
}
],
"gene_symbol": "PTPN9",
"gene_hgnc_id": 9661,
"dbsnp": "rs756811878",
"frequency_reference_population": 0.000010132341,
"hom_count_reference_population": 0,
"allele_count_reference_population": 16,
"gnomad_exomes_af": 0.00000981123,
"gnomad_genomes_af": 0.0000131435,
"gnomad_exomes_ac": 14,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2486441433429718,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.309,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1161,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.3,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.079,
"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": -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_002833.4",
"gene_symbol": "PTPN9",
"hgnc_id": 9661,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1150C>T",
"hgvs_p": "p.Arg384Cys"
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "XR_932482.2",
"gene_symbol": "LOC105370902",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.90-81G>A",
"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
}