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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: 13-19426462-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=19426462&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "TPTE2",
"hgnc_id": 17299,
"hgvs_c": "c.1358C>T",
"hgvs_p": "p.Pro453Leu",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_199254.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.0696,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.38,
"chr": "13",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.21562984585762024,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 522,
"aa_ref": "P",
"aa_start": 453,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2101,
"cdna_start": 1705,
"cds_end": null,
"cds_length": 1569,
"cds_start": 1358,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "NM_001395978.1",
"gene_hgnc_id": 17299,
"gene_symbol": "TPTE2",
"hgvs_c": "c.1358C>T",
"hgvs_p": "p.Pro453Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000697147.1",
"protein_coding": true,
"protein_id": "NP_001382907.1",
"strand": false,
"transcript": "NM_001395978.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 522,
"aa_ref": "P",
"aa_start": 453,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2101,
"cdna_start": 1705,
"cds_end": null,
"cds_length": 1569,
"cds_start": 1358,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000697147.1",
"gene_hgnc_id": 17299,
"gene_symbol": "TPTE2",
"hgvs_c": "c.1358C>T",
"hgvs_p": "p.Pro453Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001395978.1",
"protein_coding": true,
"protein_id": "ENSP00000513136.1",
"strand": false,
"transcript": "ENST00000697147.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 445,
"aa_ref": "P",
"aa_start": 376,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1558,
"cdna_start": 1337,
"cds_end": null,
"cds_length": 1338,
"cds_start": 1127,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000390680.2",
"gene_hgnc_id": 17299,
"gene_symbol": "TPTE2",
"hgvs_c": "c.1127C>T",
"hgvs_p": "p.Pro376Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000375098.2",
"strand": false,
"transcript": "ENST00000390680.2",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 522,
"aa_ref": "P",
"aa_start": 453,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1965,
"cdna_start": 1569,
"cds_end": null,
"cds_length": 1569,
"cds_start": 1358,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "NM_199254.3",
"gene_hgnc_id": 17299,
"gene_symbol": "TPTE2",
"hgvs_c": "c.1358C>T",
"hgvs_p": "p.Pro453Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_954863.2",
"strand": false,
"transcript": "NM_199254.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 522,
"aa_ref": "P",
"aa_start": 453,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1998,
"cdna_start": 1602,
"cds_end": null,
"cds_length": 1569,
"cds_start": 1358,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000696858.2",
"gene_hgnc_id": 17299,
"gene_symbol": "TPTE2",
"hgvs_c": "c.1358C>T",
"hgvs_p": "p.Pro453Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000512931.1",
"strand": false,
"transcript": "ENST00000696858.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 522,
"aa_ref": "P",
"aa_start": 453,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1790,
"cdna_start": 1569,
"cds_end": null,
"cds_length": 1569,
"cds_start": 1358,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000696988.1",
"gene_hgnc_id": 17299,
"gene_symbol": "TPTE2",
"hgvs_c": "c.1358C>T",
"hgvs_p": "p.Pro453Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000513024.1",
"strand": false,
"transcript": "ENST00000696988.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 482,
"aa_ref": "P",
"aa_start": 413,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1677,
"cdna_start": 1281,
"cds_end": null,
"cds_length": 1449,
"cds_start": 1238,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000382978.5",
"gene_hgnc_id": 17299,
"gene_symbol": "TPTE2",
"hgvs_c": "c.1238C>T",
"hgvs_p": "p.Pro413Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000372438.1",
"strand": false,
"transcript": "ENST00000382978.5",
"transcript_support_level": 5
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 445,
"aa_ref": "P",
"aa_start": 376,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1734,
"cdna_start": 1338,
"cds_end": null,
"cds_length": 1338,
"cds_start": 1127,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "NM_130785.4",
"gene_hgnc_id": 17299,
"gene_symbol": "TPTE2",
"hgvs_c": "c.1127C>T",
"hgvs_p": "p.Pro376Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_570141.3",
"strand": false,
"transcript": "NM_130785.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 411,
"aa_ref": "P",
"aa_start": 342,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1824,
"cdna_start": 1428,
"cds_end": null,
"cds_length": 1236,
"cds_start": 1025,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_001141968.2",
"gene_hgnc_id": 17299,
"gene_symbol": "TPTE2",
"hgvs_c": "c.1025C>T",
"hgvs_p": "p.Pro342Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001135440.1",
"strand": false,
"transcript": "NM_001141968.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 411,
"aa_ref": "P",
"aa_start": 342,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1800,
"cdna_start": 1410,
"cds_end": null,
"cds_length": 1236,
"cds_start": 1025,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000400103.7",
"gene_hgnc_id": 17299,
"gene_symbol": "TPTE2",
"hgvs_c": "c.1025C>T",
"hgvs_p": "p.Pro342Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000382974.2",
"strand": false,
"transcript": "ENST00000400103.7",
"transcript_support_level": 5
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 193,
"aa_ref": "P",
"aa_start": 124,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1103,
"cdna_start": 707,
"cds_end": null,
"cds_length": 582,
"cds_start": 371,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001271850.2",
"gene_hgnc_id": 17299,
"gene_symbol": "TPTE2",
"hgvs_c": "c.371C>T",
"hgvs_p": "p.Pro124Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001258779.1",
"strand": false,
"transcript": "NM_001271850.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 393,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1763,
"cdna_start": null,
"cds_end": null,
"cds_length": 1182,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 19,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000696857.1",
"gene_hgnc_id": 17299,
"gene_symbol": "TPTE2",
"hgvs_c": "c.1009-1445C>T",
"hgvs_p": null,
"intron_rank": 17,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000512930.1",
"strand": false,
"transcript": "ENST00000696857.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1965,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 24,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000696859.1",
"gene_hgnc_id": 17299,
"gene_symbol": "TPTE2",
"hgvs_c": "n.1358C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000512932.1",
"strand": false,
"transcript": "ENST00000696859.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2204,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 24,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "NR_073485.2",
"gene_hgnc_id": 17299,
"gene_symbol": "TPTE2",
"hgvs_c": "n.1681C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_073485.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1502,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 15,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NR_073487.2",
"gene_hgnc_id": 17299,
"gene_symbol": "TPTE2",
"hgvs_c": "n.1106C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_073487.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1220,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000462409.5",
"gene_hgnc_id": 17299,
"gene_symbol": "TPTE2",
"hgvs_c": "n.910-629C>T",
"hgvs_p": null,
"intron_rank": 13,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000432402.1",
"strand": false,
"transcript": "ENST00000462409.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1438,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_073486.1",
"gene_hgnc_id": 17299,
"gene_symbol": "TPTE2",
"hgvs_c": "n.953-629C>T",
"hgvs_p": null,
"intron_rank": 13,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_073486.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": null,
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 17299,
"gene_symbol": "TPTE2",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.101,
"pos": 19426462,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.236,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_199254.3"
}
]
}