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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: 1-198741991-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=198741991&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 198741991,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000442510.8",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2526C>T",
"hgvs_p": "p.Ser842Ser",
"transcript": "NM_002838.5",
"protein_id": "NP_002829.3",
"transcript_support_level": null,
"aa_start": 842,
"aa_end": null,
"aa_length": 1306,
"cds_start": 2526,
"cds_end": null,
"cds_length": 3921,
"cdna_start": 2667,
"cdna_end": null,
"cdna_length": 5357,
"mane_select": "ENST00000442510.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2526C>T",
"hgvs_p": "p.Ser842Ser",
"transcript": "ENST00000442510.8",
"protein_id": "ENSP00000411355.3",
"transcript_support_level": 1,
"aa_start": 842,
"aa_end": null,
"aa_length": 1306,
"cds_start": 2526,
"cds_end": null,
"cds_length": 3921,
"cdna_start": 2667,
"cdna_end": null,
"cdna_length": 5357,
"mane_select": "NM_002838.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2043C>T",
"hgvs_p": "p.Ser681Ser",
"transcript": "ENST00000348564.12",
"protein_id": "ENSP00000306782.7",
"transcript_support_level": 1,
"aa_start": 681,
"aa_end": null,
"aa_length": 1145,
"cds_start": 2043,
"cds_end": null,
"cds_length": 3438,
"cdna_start": 2256,
"cdna_end": null,
"cdna_length": 6812,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2241C>T",
"hgvs_p": "p.Ser747Ser",
"transcript": "ENST00000697631.1",
"protein_id": "ENSP00000513363.1",
"transcript_support_level": null,
"aa_start": 747,
"aa_end": null,
"aa_length": 1211,
"cds_start": 2241,
"cds_end": null,
"cds_length": 3636,
"cdna_start": 2327,
"cdna_end": null,
"cdna_length": 4699,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2043C>T",
"hgvs_p": "p.Ser681Ser",
"transcript": "NM_080921.4",
"protein_id": "NP_563578.2",
"transcript_support_level": null,
"aa_start": 681,
"aa_end": null,
"aa_length": 1145,
"cds_start": 2043,
"cds_end": null,
"cds_length": 3438,
"cdna_start": 2184,
"cdna_end": null,
"cdna_length": 4874,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.1488C>T",
"hgvs_p": "p.Ser496Ser",
"transcript": "ENST00000697632.1",
"protein_id": "ENSP00000513364.1",
"transcript_support_level": null,
"aa_start": 496,
"aa_end": null,
"aa_length": 960,
"cds_start": 1488,
"cds_end": null,
"cds_length": 2883,
"cdna_start": 2012,
"cdna_end": null,
"cdna_length": 4407,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2526C>T",
"hgvs_p": "p.Ser842Ser",
"transcript": "XM_047426381.1",
"protein_id": "XP_047282337.1",
"transcript_support_level": null,
"aa_start": 842,
"aa_end": null,
"aa_length": 1306,
"cds_start": 2526,
"cds_end": null,
"cds_length": 3921,
"cdna_start": 2643,
"cdna_end": null,
"cdna_length": 5333,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2382C>T",
"hgvs_p": "p.Ser794Ser",
"transcript": "XM_006711472.5",
"protein_id": "XP_006711535.1",
"transcript_support_level": null,
"aa_start": 794,
"aa_end": null,
"aa_length": 1258,
"cds_start": 2382,
"cds_end": null,
"cds_length": 3777,
"cdna_start": 2523,
"cdna_end": null,
"cdna_length": 5213,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2328C>T",
"hgvs_p": "p.Ser776Ser",
"transcript": "XM_006711473.4",
"protein_id": "XP_006711536.1",
"transcript_support_level": null,
"aa_start": 776,
"aa_end": null,
"aa_length": 1240,
"cds_start": 2328,
"cds_end": null,
"cds_length": 3723,
"cdna_start": 2469,
"cdna_end": null,
"cdna_length": 5159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2328C>T",
"hgvs_p": "p.Ser776Ser",
"transcript": "XM_047426398.1",
"protein_id": "XP_047282354.1",
"transcript_support_level": null,
"aa_start": 776,
"aa_end": null,
"aa_length": 1240,
"cds_start": 2328,
"cds_end": null,
"cds_length": 3723,
"cdna_start": 2445,
"cdna_end": null,
"cdna_length": 5135,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2184C>T",
"hgvs_p": "p.Ser728Ser",
"transcript": "XM_006711474.4",
"protein_id": "XP_006711537.1",
"transcript_support_level": null,
"aa_start": 728,
"aa_end": null,
"aa_length": 1192,
"cds_start": 2184,
"cds_end": null,
"cds_length": 3579,
"cdna_start": 2325,
"cdna_end": null,
"cdna_length": 5015,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2184C>T",
"hgvs_p": "p.Ser728Ser",
"transcript": "XM_047426409.1",
"protein_id": "XP_047282365.1",
"transcript_support_level": null,
"aa_start": 728,
"aa_end": null,
"aa_length": 1192,
"cds_start": 2184,
"cds_end": null,
"cds_length": 3579,
"cdna_start": 2301,
"cdna_end": null,
"cdna_length": 4991,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.2043C>T",
"hgvs_p": "p.Ser681Ser",
"transcript": "XM_047426415.1",
"protein_id": "XP_047282371.1",
"transcript_support_level": null,
"aa_start": 681,
"aa_end": null,
"aa_length": 1145,
"cds_start": 2043,
"cds_end": null,
"cds_length": 3438,
"cdna_start": 2160,
"cdna_end": null,
"cdna_length": 4850,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.645C>T",
"hgvs_p": "p.Ser215Ser",
"transcript": "XM_047426417.1",
"protein_id": "XP_047282373.1",
"transcript_support_level": null,
"aa_start": 215,
"aa_end": null,
"aa_length": 679,
"cds_start": 645,
"cds_end": null,
"cds_length": 2040,
"cdna_start": 846,
"cdna_end": null,
"cdna_length": 3536,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.645C>T",
"hgvs_p": "p.Ser215Ser",
"transcript": "XM_047426420.1",
"protein_id": "XP_047282376.1",
"transcript_support_level": null,
"aa_start": 215,
"aa_end": null,
"aa_length": 679,
"cds_start": 645,
"cds_end": null,
"cds_length": 2040,
"cdna_start": 737,
"cdna_end": null,
"cdna_length": 3427,
"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": 13,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "n.1579C>T",
"hgvs_p": null,
"transcript": "ENST00000491302.2",
"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": 3951,
"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": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "n.6356C>T",
"hgvs_p": null,
"transcript": "ENST00000697630.1",
"protein_id": null,
"transcript_support_level": null,
"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": 7205,
"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": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "n.*747C>T",
"hgvs_p": null,
"transcript": "ENST00000697633.1",
"protein_id": "ENSP00000513365.1",
"transcript_support_level": null,
"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": 3630,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MIR181A1HG",
"gene_hgnc_id": 48659,
"hgvs_c": "n.451G>A",
"hgvs_p": null,
"transcript": "ENST00000806890.1",
"protein_id": null,
"transcript_support_level": null,
"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": 679,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "n.*747C>T",
"hgvs_p": null,
"transcript": "ENST00000697633.1",
"protein_id": "ENSP00000513365.1",
"transcript_support_level": null,
"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": 3630,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"dbsnp": "rs373509702",
"frequency_reference_population": 0.000018636434,
"hom_count_reference_population": 0,
"allele_count_reference_population": 30,
"gnomad_exomes_af": 0.000016445,
"gnomad_genomes_af": 0.000039909,
"gnomad_exomes_ac": 24,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.23999999463558197,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.24,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.874,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.07,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Very_Strong,BP7",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 11,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Very_Strong",
"BP7"
],
"verdict": "Benign",
"transcript": "ENST00000442510.8",
"gene_symbol": "PTPRC",
"hgnc_id": 9666,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2526C>T",
"hgvs_p": "p.Ser842Ser"
},
{
"score": -8,
"benign_score": 10,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Very_Strong"
],
"verdict": "Benign",
"transcript": "ENST00000806890.1",
"gene_symbol": "MIR181A1HG",
"hgnc_id": 48659,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.451G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Immunodeficiency 104,not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "not specified|Immunodeficiency 104",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}