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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: 14-88468307-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=88468307&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 88468307,
"ref": "G",
"alt": "C",
"effect": "intron_variant",
"transcript": "ENST00000556564.6",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.3397-42C>G",
"hgvs_p": null,
"transcript": "NM_007039.4",
"protein_id": "NP_008970.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1174,
"cds_start": -4,
"cds_end": null,
"cds_length": 3525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6443,
"mane_select": "ENST00000556564.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.3397-42C>G",
"hgvs_p": null,
"transcript": "ENST00000556564.6",
"protein_id": "ENSP00000452414.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1174,
"cds_start": -4,
"cds_end": null,
"cds_length": 3525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6443,
"mane_select": "NM_007039.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.3397-42C>G",
"hgvs_p": null,
"transcript": "ENST00000328736.7",
"protein_id": "ENSP00000330276.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1174,
"cds_start": -4,
"cds_end": null,
"cds_length": 3525,
"cdna_start": null,
"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": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "n.*3334-42C>G",
"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": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "n.3698-42C>G",
"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": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.209-42C>G",
"hgvs_p": null,
"transcript": "ENST00000553531.1",
"protein_id": "ENSP00000450847.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 128,
"cds_start": -4,
"cds_end": null,
"cds_length": 387,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 704,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "c.253-1540G>C",
"hgvs_p": null,
"transcript": "ENST00000556406.5",
"protein_id": "ENSP00000450809.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 90,
"cds_start": -4,
"cds_end": null,
"cds_length": 273,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 758,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.3397-42C>G",
"hgvs_p": null,
"transcript": "XM_005267287.4",
"protein_id": "XP_005267344.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1174,
"cds_start": -4,
"cds_end": null,
"cds_length": 3525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6327,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.3397-42C>G",
"hgvs_p": null,
"transcript": "XM_011536367.4",
"protein_id": "XP_011534669.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1174,
"cds_start": -4,
"cds_end": null,
"cds_length": 3525,
"cdna_start": null,
"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": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.3028-42C>G",
"hgvs_p": null,
"transcript": "XM_011536368.3",
"protein_id": "XP_011534670.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1051,
"cds_start": -4,
"cds_end": null,
"cds_length": 3156,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5625,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.2785-42C>G",
"hgvs_p": null,
"transcript": "XM_017020939.2",
"protein_id": "XP_016876428.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 970,
"cds_start": -4,
"cds_end": null,
"cds_length": 2913,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5755,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "c.1285-1540G>C",
"hgvs_p": null,
"transcript": "XM_006720205.2",
"protein_id": "XP_006720268.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 434,
"cds_start": -4,
"cds_end": null,
"cds_length": 1305,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1950,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "c.1282-1540G>C",
"hgvs_p": null,
"transcript": "XM_047431581.1",
"protein_id": "XP_047287537.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 433,
"cds_start": -4,
"cds_end": null,
"cds_length": 1302,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1947,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "c.1186-1540G>C",
"hgvs_p": null,
"transcript": "XM_047431584.1",
"protein_id": "XP_047287540.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 401,
"cds_start": -4,
"cds_end": null,
"cds_length": 1206,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1851,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"dbsnp": "rs366476",
"frequency_reference_population": 0.00000288145,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000288145,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8600000143051147,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.86,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.356,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000556564.6",
"gene_symbol": "PTPN21",
"hgnc_id": 9651,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3397-42C>G",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000556406.5",
"gene_symbol": "SPATA7",
"hgnc_id": 20423,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.253-1540G>C",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}