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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: 20-42380098-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=42380098&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 42380098,
"ref": "C",
"alt": "G",
"effect": "intron_variant",
"transcript": "ENST00000373193.7",
"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": 31,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPRT",
"gene_hgnc_id": 9682,
"hgvs_c": "c.1561-27813G>C",
"hgvs_p": null,
"transcript": "NM_007050.6",
"protein_id": "NP_008981.4",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1441,
"cds_start": -4,
"cds_end": null,
"cds_length": 4326,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12622,
"mane_select": "ENST00000373187.6",
"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": 31,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPRT",
"gene_hgnc_id": 9682,
"hgvs_c": "c.1561-27813G>C",
"hgvs_p": null,
"transcript": "ENST00000373187.6",
"protein_id": "ENSP00000362283.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1441,
"cds_start": -4,
"cds_end": null,
"cds_length": 4326,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12622,
"mane_select": "NM_007050.6",
"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": 32,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPRT",
"gene_hgnc_id": 9682,
"hgvs_c": "c.1561-27813G>C",
"hgvs_p": null,
"transcript": "ENST00000373193.7",
"protein_id": "ENSP00000362289.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1463,
"cds_start": -4,
"cds_end": null,
"cds_length": 4392,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12681,
"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": 32,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPRT",
"gene_hgnc_id": 9682,
"hgvs_c": "c.1561-27813G>C",
"hgvs_p": null,
"transcript": "ENST00000373198.8",
"protein_id": "ENSP00000362294.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1460,
"cds_start": -4,
"cds_end": null,
"cds_length": 4383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12746,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPRT",
"gene_hgnc_id": 9682,
"hgvs_c": "n.*1419-27813G>C",
"hgvs_p": null,
"transcript": "ENST00000617474.1",
"protein_id": "ENSP00000484248.1",
"transcript_support_level": 5,
"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": 4521,
"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": 32,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPRT",
"gene_hgnc_id": 9682,
"hgvs_c": "c.1561-27813G>C",
"hgvs_p": null,
"transcript": "NM_001394024.1",
"protein_id": "NP_001380953.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1460,
"cds_start": -4,
"cds_end": null,
"cds_length": 4383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12679,
"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": 32,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPRT",
"gene_hgnc_id": 9682,
"hgvs_c": "c.1561-27813G>C",
"hgvs_p": null,
"transcript": "NM_133170.4",
"protein_id": "NP_573400.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1460,
"cds_start": -4,
"cds_end": null,
"cds_length": 4383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12679,
"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": 31,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPRT",
"gene_hgnc_id": 9682,
"hgvs_c": "c.1561-27813G>C",
"hgvs_p": null,
"transcript": "ENST00000373184.5",
"protein_id": "ENSP00000362280.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1451,
"cds_start": -4,
"cds_end": null,
"cds_length": 4356,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12483,
"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": 31,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPRT",
"gene_hgnc_id": 9682,
"hgvs_c": "c.1561-27813G>C",
"hgvs_p": null,
"transcript": "ENST00000356100.6",
"protein_id": "ENSP00000348408.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1450,
"cds_start": -4,
"cds_end": null,
"cds_length": 4353,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12480,
"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": 31,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPRT",
"gene_hgnc_id": 9682,
"hgvs_c": "c.1561-27813G>C",
"hgvs_p": null,
"transcript": "NM_001394025.1",
"protein_id": "NP_001380954.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1449,
"cds_start": -4,
"cds_end": null,
"cds_length": 4350,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12646,
"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": 31,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPRT",
"gene_hgnc_id": 9682,
"hgvs_c": "c.1561-27813G>C",
"hgvs_p": null,
"transcript": "ENST00000373190.5",
"protein_id": "ENSP00000362286.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1440,
"cds_start": -4,
"cds_end": null,
"cds_length": 4323,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12559,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPRT",
"gene_hgnc_id": 9682,
"hgvs_c": "c.1561-27813G>C",
"hgvs_p": null,
"transcript": "ENST00000373201.5",
"protein_id": "ENSP00000362297.1",
"transcript_support_level": 5,
"aa_start": null,
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"aa_length": 1431,
"cds_start": -4,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 27,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPRT",
"gene_hgnc_id": 9682,
"hgvs_c": "c.1561-27813G>C",
"hgvs_p": null,
"transcript": "NM_001394026.1",
"protein_id": "NP_001380955.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": 1289,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPRT",
"gene_hgnc_id": 9682,
"hgvs_c": "c.1576-27813G>C",
"hgvs_p": null,
"transcript": "XM_017027611.2",
"protein_id": "XP_016883100.1",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": -4,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPRT",
"gene_hgnc_id": 9682,
"hgvs_c": "c.1576-27813G>C",
"hgvs_p": null,
"transcript": "XM_017027612.2",
"protein_id": "XP_016883101.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1455,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 12723,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPRT",
"gene_hgnc_id": 9682,
"hgvs_c": "c.1576-27813G>C",
"hgvs_p": null,
"transcript": "XM_047439846.1",
"protein_id": "XP_047295802.1",
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},
{
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"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 31,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPRT",
"gene_hgnc_id": 9682,
"hgvs_c": "c.1576-27813G>C",
"hgvs_p": null,
"transcript": "XM_047439847.1",
"protein_id": "XP_047295803.1",
"transcript_support_level": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPRT",
"gene_hgnc_id": 9682,
"hgvs_c": "c.1561-27813G>C",
"hgvs_p": null,
"transcript": "XM_047439848.1",
"protein_id": "XP_047295804.1",
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"cdna_start": null,
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"mane_select": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PTPRT",
"gene_hgnc_id": 9682,
"hgvs_c": "c.1576-27813G>C",
"hgvs_p": null,
"transcript": "XM_017027613.2",
"protein_id": "XP_016883102.1",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 12665,
"mane_select": null,
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"biotype": null,
"feature": null
}
],
"gene_symbol": "PTPRT",
"gene_hgnc_id": 9682,
"dbsnp": "rs10485691",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8299999833106995,
"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": -0.83,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.026,
"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": "ENST00000373193.7",
"gene_symbol": "PTPRT",
"hgnc_id": 9682,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1561-27813G>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
}