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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: 12-6957662-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=6957662&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 6957662,
"ref": "C",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000318974.14",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN6",
"gene_hgnc_id": 9658,
"hgvs_c": "c.1083C>A",
"hgvs_p": "p.Cys361*",
"transcript": "NM_002831.6",
"protein_id": "NP_002822.2",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 595,
"cds_start": 1083,
"cds_end": null,
"cds_length": 1788,
"cdna_start": 1240,
"cdna_end": null,
"cdna_length": 2161,
"mane_select": "ENST00000318974.14",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN6",
"gene_hgnc_id": 9658,
"hgvs_c": "c.1083C>A",
"hgvs_p": "p.Cys361*",
"transcript": "ENST00000318974.14",
"protein_id": "ENSP00000326010.9",
"transcript_support_level": 1,
"aa_start": 361,
"aa_end": null,
"aa_length": 595,
"cds_start": 1083,
"cds_end": null,
"cds_length": 1788,
"cdna_start": 1240,
"cdna_end": null,
"cdna_length": 2161,
"mane_select": "NM_002831.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN6",
"gene_hgnc_id": 9658,
"hgvs_c": "c.1083C>A",
"hgvs_p": "p.Cys361*",
"transcript": "ENST00000456013.5",
"protein_id": "ENSP00000391592.1",
"transcript_support_level": 1,
"aa_start": 361,
"aa_end": null,
"aa_length": 624,
"cds_start": 1083,
"cds_end": null,
"cds_length": 1875,
"cdna_start": 1325,
"cdna_end": null,
"cdna_length": 2389,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN6",
"gene_hgnc_id": 9658,
"hgvs_c": "c.1089C>A",
"hgvs_p": "p.Cys363*",
"transcript": "ENST00000399448.5",
"protein_id": "ENSP00000382376.1",
"transcript_support_level": 1,
"aa_start": 363,
"aa_end": null,
"aa_length": 597,
"cds_start": 1089,
"cds_end": null,
"cds_length": 1794,
"cdna_start": 1238,
"cdna_end": null,
"cdna_length": 2159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN6",
"gene_hgnc_id": 9658,
"hgvs_c": "c.1083C>A",
"hgvs_p": "p.Cys361*",
"transcript": "NM_080549.4",
"protein_id": "NP_536859.1",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 624,
"cds_start": 1083,
"cds_end": null,
"cds_length": 1875,
"cdna_start": 1240,
"cdna_end": null,
"cdna_length": 2304,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN6",
"gene_hgnc_id": 9658,
"hgvs_c": "c.1089C>A",
"hgvs_p": "p.Cys363*",
"transcript": "NM_080548.5",
"protein_id": "NP_536858.1",
"transcript_support_level": null,
"aa_start": 363,
"aa_end": null,
"aa_length": 597,
"cds_start": 1089,
"cds_end": null,
"cds_length": 1794,
"cdna_start": 1238,
"cdna_end": null,
"cdna_length": 2159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN6",
"gene_hgnc_id": 9658,
"hgvs_c": "c.1089C>A",
"hgvs_p": "p.Cys363*",
"transcript": "XM_011520988.2",
"protein_id": "XP_011519290.1",
"transcript_support_level": null,
"aa_start": 363,
"aa_end": null,
"aa_length": 597,
"cds_start": 1089,
"cds_end": null,
"cds_length": 1794,
"cdna_start": 1238,
"cdna_end": null,
"cdna_length": 2150,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN6",
"gene_hgnc_id": 9658,
"hgvs_c": "c.1083C>A",
"hgvs_p": "p.Cys361*",
"transcript": "XM_024449106.1",
"protein_id": "XP_024304874.1",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 595,
"cds_start": 1083,
"cds_end": null,
"cds_length": 1788,
"cdna_start": 1240,
"cdna_end": null,
"cdna_length": 2152,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN6",
"gene_hgnc_id": 9658,
"hgvs_c": "c.972C>A",
"hgvs_p": "p.Cys324*",
"transcript": "XM_047429231.1",
"protein_id": "XP_047285187.1",
"transcript_support_level": null,
"aa_start": 324,
"aa_end": null,
"aa_length": 558,
"cds_start": 972,
"cds_end": null,
"cds_length": 1677,
"cdna_start": 1121,
"cdna_end": null,
"cdna_length": 2042,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN6",
"gene_hgnc_id": 9658,
"hgvs_c": "c.966C>A",
"hgvs_p": "p.Cys322*",
"transcript": "XM_047429232.1",
"protein_id": "XP_047285188.1",
"transcript_support_level": null,
"aa_start": 322,
"aa_end": null,
"aa_length": 556,
"cds_start": 966,
"cds_end": null,
"cds_length": 1671,
"cdna_start": 1123,
"cdna_end": null,
"cdna_length": 2044,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN6",
"gene_hgnc_id": 9658,
"hgvs_c": "n.1491C>A",
"hgvs_p": null,
"transcript": "ENST00000416215.6",
"protein_id": null,
"transcript_support_level": 2,
"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": 2412,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTPN6",
"gene_hgnc_id": 9658,
"dbsnp": "rs190247406",
"frequency_reference_population": 8.034426e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 8.03443e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5099999904632568,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.51,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.55,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PVS1",
"PM2"
],
"verdict": "Pathogenic",
"transcript": "ENST00000318974.14",
"gene_symbol": "PTPN6",
"hgnc_id": 9658,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1083C>A",
"hgvs_p": "p.Cys361*"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}