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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: 1-198713049-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=198713049&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 198713049,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000442510.8",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.1268C>T",
"hgvs_p": "p.Thr423Ile",
"transcript": "NM_002838.5",
"protein_id": "NP_002829.3",
"transcript_support_level": null,
"aa_start": 423,
"aa_end": null,
"aa_length": 1306,
"cds_start": 1268,
"cds_end": null,
"cds_length": 3921,
"cdna_start": 1409,
"cdna_end": null,
"cdna_length": 5357,
"mane_select": "ENST00000442510.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.1268C>T",
"hgvs_p": "p.Thr423Ile",
"transcript": "ENST00000442510.8",
"protein_id": "ENSP00000411355.3",
"transcript_support_level": 1,
"aa_start": 423,
"aa_end": null,
"aa_length": 1306,
"cds_start": 1268,
"cds_end": null,
"cds_length": 3921,
"cdna_start": 1409,
"cdna_end": null,
"cdna_length": 5357,
"mane_select": "NM_002838.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.785C>T",
"hgvs_p": "p.Thr262Ile",
"transcript": "ENST00000348564.12",
"protein_id": "ENSP00000306782.7",
"transcript_support_level": 1,
"aa_start": 262,
"aa_end": null,
"aa_length": 1145,
"cds_start": 785,
"cds_end": null,
"cds_length": 3438,
"cdna_start": 998,
"cdna_end": null,
"cdna_length": 6812,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.926C>T",
"hgvs_p": "p.Thr309Ile",
"transcript": "ENST00000530727.5",
"protein_id": "ENSP00000433536.2",
"transcript_support_level": 1,
"aa_start": 309,
"aa_end": null,
"aa_length": 599,
"cds_start": 926,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 1088,
"cdna_end": null,
"cdna_length": 1962,
"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": 11,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "n.1124C>T",
"hgvs_p": null,
"transcript": "ENST00000529828.5",
"protein_id": "ENSP00000469141.1",
"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": 2336,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.983C>T",
"hgvs_p": "p.Thr328Ile",
"transcript": "ENST00000697631.1",
"protein_id": "ENSP00000513363.1",
"transcript_support_level": null,
"aa_start": 328,
"aa_end": null,
"aa_length": 1211,
"cds_start": 983,
"cds_end": null,
"cds_length": 3636,
"cdna_start": 1069,
"cdna_end": null,
"cdna_length": 4699,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.785C>T",
"hgvs_p": "p.Thr262Ile",
"transcript": "NM_080921.4",
"protein_id": "NP_563578.2",
"transcript_support_level": null,
"aa_start": 262,
"aa_end": null,
"aa_length": 1145,
"cds_start": 785,
"cds_end": null,
"cds_length": 3438,
"cdna_start": 926,
"cdna_end": null,
"cdna_length": 4874,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.230C>T",
"hgvs_p": "p.Thr77Ile",
"transcript": "ENST00000697632.1",
"protein_id": "ENSP00000513364.1",
"transcript_support_level": null,
"aa_start": 77,
"aa_end": null,
"aa_length": 960,
"cds_start": 230,
"cds_end": null,
"cds_length": 2883,
"cdna_start": 754,
"cdna_end": null,
"cdna_length": 4407,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.1070C>T",
"hgvs_p": "p.Thr357Ile",
"transcript": "ENST00000367367.8",
"protein_id": "ENSP00000356337.5",
"transcript_support_level": 2,
"aa_start": 357,
"aa_end": null,
"aa_length": 734,
"cds_start": 1070,
"cds_end": null,
"cds_length": 2205,
"cdna_start": 1156,
"cdna_end": null,
"cdna_length": 2291,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.1268C>T",
"hgvs_p": "p.Thr423Ile",
"transcript": "XM_047426381.1",
"protein_id": "XP_047282337.1",
"transcript_support_level": null,
"aa_start": 423,
"aa_end": null,
"aa_length": 1306,
"cds_start": 1268,
"cds_end": null,
"cds_length": 3921,
"cdna_start": 1385,
"cdna_end": null,
"cdna_length": 5333,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.1124C>T",
"hgvs_p": "p.Thr375Ile",
"transcript": "XM_006711472.5",
"protein_id": "XP_006711535.1",
"transcript_support_level": null,
"aa_start": 375,
"aa_end": null,
"aa_length": 1258,
"cds_start": 1124,
"cds_end": null,
"cds_length": 3777,
"cdna_start": 1265,
"cdna_end": null,
"cdna_length": 5213,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.1070C>T",
"hgvs_p": "p.Thr357Ile",
"transcript": "XM_006711473.4",
"protein_id": "XP_006711536.1",
"transcript_support_level": null,
"aa_start": 357,
"aa_end": null,
"aa_length": 1240,
"cds_start": 1070,
"cds_end": null,
"cds_length": 3723,
"cdna_start": 1211,
"cdna_end": null,
"cdna_length": 5159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.1070C>T",
"hgvs_p": "p.Thr357Ile",
"transcript": "XM_047426398.1",
"protein_id": "XP_047282354.1",
"transcript_support_level": null,
"aa_start": 357,
"aa_end": null,
"aa_length": 1240,
"cds_start": 1070,
"cds_end": null,
"cds_length": 3723,
"cdna_start": 1187,
"cdna_end": null,
"cdna_length": 5135,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.926C>T",
"hgvs_p": "p.Thr309Ile",
"transcript": "XM_006711474.4",
"protein_id": "XP_006711537.1",
"transcript_support_level": null,
"aa_start": 309,
"aa_end": null,
"aa_length": 1192,
"cds_start": 926,
"cds_end": null,
"cds_length": 3579,
"cdna_start": 1067,
"cdna_end": null,
"cdna_length": 5015,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.926C>T",
"hgvs_p": "p.Thr309Ile",
"transcript": "XM_047426409.1",
"protein_id": "XP_047282365.1",
"transcript_support_level": null,
"aa_start": 309,
"aa_end": null,
"aa_length": 1192,
"cds_start": 926,
"cds_end": null,
"cds_length": 3579,
"cdna_start": 1043,
"cdna_end": null,
"cdna_length": 4991,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "c.785C>T",
"hgvs_p": "p.Thr262Ile",
"transcript": "XM_047426415.1",
"protein_id": "XP_047282371.1",
"transcript_support_level": null,
"aa_start": 262,
"aa_end": null,
"aa_length": 1145,
"cds_start": 785,
"cds_end": null,
"cds_length": 3438,
"cdna_start": 902,
"cdna_end": null,
"cdna_length": 4850,
"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": 1,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "n.321C>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": 7,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"hgvs_c": "n.5098C>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
}
],
"gene_symbol": "PTPRC",
"gene_hgnc_id": 9666,
"dbsnp": "rs6696162",
"frequency_reference_population": 0.0012735451,
"hom_count_reference_population": 22,
"allele_count_reference_population": 2055,
"gnomad_exomes_af": 0.000693188,
"gnomad_genomes_af": 0.00684437,
"gnomad_exomes_ac": 1013,
"gnomad_genomes_ac": 1042,
"gnomad_exomes_homalt": 11,
"gnomad_genomes_homalt": 11,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.003383129835128784,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.13,
"revel_prediction": "Benign",
"alphamissense_score": 0.1695,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.43,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -8.218,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000442510.8",
"gene_symbol": "PTPRC",
"hgnc_id": 9666,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1268C>T",
"hgvs_p": "p.Thr423Ile"
}
],
"clinvar_disease": "Immunodeficiency 104,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:1",
"phenotype_combined": "not specified|Immunodeficiency 104",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}