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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: 7-121888781-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=121888781&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 121888781,
"ref": "T",
"alt": "C",
"effect": "intron_variant",
"transcript": "ENST00000393386.7",
"consequences": [
{
"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": 30,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTPRZ1",
"gene_hgnc_id": 9685,
"hgvs_c": "c.58+15224T>C",
"hgvs_p": null,
"transcript": "NM_002851.3",
"protein_id": "NP_002842.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2315,
"cds_start": -4,
"cds_end": null,
"cds_length": 6948,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8103,
"mane_select": "ENST00000393386.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTPRZ1",
"gene_hgnc_id": 9685,
"hgvs_c": "c.58+15224T>C",
"hgvs_p": null,
"transcript": "ENST00000393386.7",
"protein_id": "ENSP00000377047.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 2315,
"cds_start": -4,
"cds_end": null,
"cds_length": 6948,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8103,
"mane_select": "NM_002851.3",
"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": 29,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTPRZ1",
"gene_hgnc_id": 9685,
"hgvs_c": "c.58+15224T>C",
"hgvs_p": null,
"transcript": "ENST00000449182.1",
"protein_id": "ENSP00000410000.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1448,
"cds_start": -4,
"cds_end": null,
"cds_length": 4347,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4627,
"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": 31,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTPRZ1",
"gene_hgnc_id": 9685,
"hgvs_c": "c.58+15224T>C",
"hgvs_p": null,
"transcript": "ENST00000651863.1",
"protein_id": "ENSP00000498439.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2354,
"cds_start": -4,
"cds_end": null,
"cds_length": 7065,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7840,
"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": 30,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTPRZ1",
"gene_hgnc_id": 9685,
"hgvs_c": "c.58+15224T>C",
"hgvs_p": null,
"transcript": "ENST00000651320.1",
"protein_id": "ENSP00000498388.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2347,
"cds_start": -4,
"cds_end": null,
"cds_length": 7044,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7822,
"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": 29,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTPRZ1",
"gene_hgnc_id": 9685,
"hgvs_c": "c.58+15224T>C",
"hgvs_p": null,
"transcript": "NM_001369395.1",
"protein_id": "NP_001356324.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2308,
"cds_start": -4,
"cds_end": null,
"cds_length": 6927,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8082,
"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": 29,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTPRZ1",
"gene_hgnc_id": 9685,
"hgvs_c": "c.58+15224T>C",
"hgvs_p": null,
"transcript": "ENST00000652298.1",
"protein_id": "ENSP00000499137.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2308,
"cds_start": -4,
"cds_end": null,
"cds_length": 6927,
"cdna_start": null,
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"cdna_length": 7866,
"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": 31,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTPRZ1",
"gene_hgnc_id": 9685,
"hgvs_c": "c.-87-4743T>C",
"hgvs_p": null,
"transcript": "NM_001369396.1",
"protein_id": "NP_001356325.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2301,
"cds_start": -4,
"cds_end": null,
"cds_length": 6906,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8206,
"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": 31,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTPRZ1",
"gene_hgnc_id": 9685,
"hgvs_c": "c.58+15224T>C",
"hgvs_p": null,
"transcript": "ENST00000650681.1",
"protein_id": "ENSP00000498708.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2059,
"cds_start": -4,
"cds_end": null,
"cds_length": 6180,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7149,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTPRZ1",
"gene_hgnc_id": 9685,
"hgvs_c": "c.58+15224T>C",
"hgvs_p": null,
"transcript": "ENST00000651390.1",
"protein_id": "ENSP00000498965.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1908,
"cds_start": -4,
"cds_end": null,
"cds_length": 5727,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6669,
"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": 32,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTPRZ1",
"gene_hgnc_id": 9685,
"hgvs_c": "c.58+15224T>C",
"hgvs_p": null,
"transcript": "ENST00000651842.1",
"protein_id": "ENSP00000499098.1",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": -4,
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},
{
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"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 31,
"intron_rank": 1,
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"gene_symbol": "PTPRZ1",
"gene_hgnc_id": 9685,
"hgvs_c": "c.58+15224T>C",
"hgvs_p": null,
"transcript": "ENST00000650826.1",
"protein_id": "ENSP00000498356.1",
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 31,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTPRZ1",
"gene_hgnc_id": 9685,
"hgvs_c": "c.58+15224T>C",
"hgvs_p": null,
"transcript": "ENST00000651065.1",
"protein_id": "ENSP00000499073.1",
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 30,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTPRZ1",
"gene_hgnc_id": 9685,
"hgvs_c": "c.58+15224T>C",
"hgvs_p": null,
"transcript": "ENST00000650728.1",
"protein_id": "ENSP00000499152.1",
"transcript_support_level": null,
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"feature": null
},
{
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"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"intron_rank": 1,
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"gene_symbol": "PTPRZ1",
"gene_hgnc_id": 9685,
"hgvs_c": "c.58+15224T>C",
"hgvs_p": null,
"transcript": "NM_001206838.2",
"protein_id": "NP_001193767.1",
"transcript_support_level": null,
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},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"intron_rank": 1,
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"gene_symbol": "PTPRZ1",
"gene_hgnc_id": 9685,
"hgvs_c": "c.58+15224T>C",
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"transcript": "NM_001206839.2",
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},
{
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"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 3,
"intron_rank": 1,
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"gene_symbol": "PTPRZ1",
"gene_hgnc_id": 9685,
"hgvs_c": "n.397+15224T>C",
"hgvs_p": null,
"transcript": "ENST00000471837.1",
"protein_id": null,
"transcript_support_level": 4,
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},
{
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"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 31,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTPRZ1",
"gene_hgnc_id": 9685,
"hgvs_c": "n.59-4743T>C",
"hgvs_p": null,
"transcript": "ENST00000652054.1",
"protein_id": "ENSP00000498722.1",
"transcript_support_level": null,
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"feature": null
}
],
"gene_symbol": "PTPRZ1",
"gene_hgnc_id": 9685,
"dbsnp": "rs1916889",
"frequency_reference_population": 0.54148567,
"hom_count_reference_population": 22902,
"allele_count_reference_population": 82282,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.541486,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 82282,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 22902,
"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": -0.048,
"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": -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": "ENST00000393386.7",
"gene_symbol": "PTPRZ1",
"hgnc_id": 9685,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.58+15224T>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
}