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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: 3-133649518-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=133649518&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "TOPBP1",
"hgnc_id": 17008,
"hgvs_c": "c.1369A>C",
"hgvs_p": "p.Lys457Gln",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -12,
"transcript": "NM_007027.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_score": -12,
"allele_count_reference_population": 1200130,
"alphamissense_prediction": null,
"alphamissense_score": 0.0635,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.79,
"chr": "3",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 8.155076898219704e-7,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1522,
"aa_ref": "K",
"aa_start": 457,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5761,
"cdna_start": 1549,
"cds_end": null,
"cds_length": 4569,
"cds_start": 1369,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_007027.4",
"gene_hgnc_id": 17008,
"gene_symbol": "TOPBP1",
"hgvs_c": "c.1369A>C",
"hgvs_p": "p.Lys457Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000260810.10",
"protein_coding": true,
"protein_id": "NP_008958.2",
"strand": false,
"transcript": "NM_007027.4",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1522,
"aa_ref": "K",
"aa_start": 457,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5761,
"cdna_start": 1549,
"cds_end": null,
"cds_length": 4569,
"cds_start": 1369,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000260810.10",
"gene_hgnc_id": 17008,
"gene_symbol": "TOPBP1",
"hgvs_c": "c.1369A>C",
"hgvs_p": "p.Lys457Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_007027.4",
"protein_coding": true,
"protein_id": "ENSP00000260810.5",
"strand": false,
"transcript": "ENST00000260810.10",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1522,
"aa_ref": "K",
"aa_start": 457,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5397,
"cdna_start": 1597,
"cds_end": null,
"cds_length": 4569,
"cds_start": 1369,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000881661.1",
"gene_hgnc_id": 17008,
"gene_symbol": "TOPBP1",
"hgvs_c": "c.1369A>C",
"hgvs_p": "p.Lys457Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551720.1",
"strand": false,
"transcript": "ENST00000881661.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1522,
"aa_ref": "K",
"aa_start": 457,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5610,
"cdna_start": 1770,
"cds_end": null,
"cds_length": 4569,
"cds_start": 1369,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000953681.1",
"gene_hgnc_id": 17008,
"gene_symbol": "TOPBP1",
"hgvs_c": "c.1369A>C",
"hgvs_p": "p.Lys457Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000623740.1",
"strand": false,
"transcript": "ENST00000953681.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1517,
"aa_ref": "K",
"aa_start": 452,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5746,
"cdna_start": 1534,
"cds_end": null,
"cds_length": 4554,
"cds_start": 1354,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001363889.2",
"gene_hgnc_id": 17008,
"gene_symbol": "TOPBP1",
"hgvs_c": "c.1354A>C",
"hgvs_p": "p.Lys452Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001350818.1",
"strand": false,
"transcript": "NM_001363889.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1517,
"aa_ref": "K",
"aa_start": 452,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6152,
"cdna_start": 1973,
"cds_end": null,
"cds_length": 4554,
"cds_start": 1354,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000642236.1",
"gene_hgnc_id": 17008,
"gene_symbol": "TOPBP1",
"hgvs_c": "c.1354A>C",
"hgvs_p": "p.Lys452Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000493612.1",
"strand": false,
"transcript": "ENST00000642236.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1517,
"aa_ref": "K",
"aa_start": 452,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4921,
"cdna_start": 1503,
"cds_end": null,
"cds_length": 4554,
"cds_start": 1354,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000881663.1",
"gene_hgnc_id": 17008,
"gene_symbol": "TOPBP1",
"hgvs_c": "c.1354A>C",
"hgvs_p": "p.Lys452Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551722.1",
"strand": false,
"transcript": "ENST00000881663.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1468,
"aa_ref": "K",
"aa_start": 457,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5103,
"cdna_start": 1468,
"cds_end": null,
"cds_length": 4407,
"cds_start": 1369,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000933452.1",
"gene_hgnc_id": 17008,
"gene_symbol": "TOPBP1",
"hgvs_c": "c.1369A>C",
"hgvs_p": "p.Lys457Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603511.1",
"strand": false,
"transcript": "ENST00000933452.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1286,
"aa_ref": "K",
"aa_start": 452,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4651,
"cdna_start": 1546,
"cds_end": null,
"cds_length": 3861,
"cds_start": 1354,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000881662.1",
"gene_hgnc_id": 17008,
"gene_symbol": "TOPBP1",
"hgvs_c": "c.1354A>C",
"hgvs_p": "p.Lys452Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551721.1",
"strand": false,
"transcript": "ENST00000881662.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1522,
"aa_ref": "K",
"aa_start": 457,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5756,
"cdna_start": 1544,
"cds_end": null,
"cds_length": 4569,
"cds_start": 1369,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_017005636.3",
"gene_hgnc_id": 17008,
"gene_symbol": "TOPBP1",
"hgvs_c": "c.1369A>C",
"hgvs_p": "p.Lys457Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016861125.1",
"strand": false,
"transcript": "XM_017005636.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
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"aa_length": 1517,
"aa_ref": "K",
"aa_start": 452,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5741,
"cdna_start": 1529,
"cds_end": null,
"cds_length": 4554,
"cds_start": 1354,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047447355.1",
"gene_hgnc_id": 17008,
"gene_symbol": "TOPBP1",
"hgvs_c": "c.1354A>C",
"hgvs_p": "p.Lys452Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047303311.1",
"strand": false,
"transcript": "XM_047447355.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
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"aa_length": 1183,
"aa_ref": "K",
"aa_start": 457,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3869,
"cdna_start": 1549,
"cds_end": null,
"cds_length": 3552,
"cds_start": 1369,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047447356.1",
"gene_hgnc_id": 17008,
"gene_symbol": "TOPBP1",
"hgvs_c": "c.1369A>C",
"hgvs_p": "p.Lys457Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047303312.1",
"strand": false,
"transcript": "XM_047447356.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
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"aa_length": 1178,
"aa_ref": "K",
"aa_start": 452,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3853,
"cdna_start": 1534,
"cds_end": null,
"cds_length": 3537,
"cds_start": 1354,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047447357.1",
"gene_hgnc_id": 17008,
"gene_symbol": "TOPBP1",
"hgvs_c": "c.1354A>C",
"hgvs_p": "p.Lys452Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047303313.1",
"strand": false,
"transcript": "XM_047447357.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1126,
"aa_ref": "K",
"aa_start": 457,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3718,
"cdna_start": 1549,
"cds_end": null,
"cds_length": 3381,
"cds_start": 1369,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_011512357.4",
"gene_hgnc_id": 17008,
"gene_symbol": "TOPBP1",
"hgvs_c": "c.1369A>C",
"hgvs_p": "p.Lys457Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011510659.1",
"strand": false,
"transcript": "XM_011512357.4",
"transcript_support_level": null
},
{
"aa_alt": "Q",
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"aa_length": 1121,
"aa_ref": "K",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3703,
"cdna_start": 1534,
"cds_end": null,
"cds_length": 3366,
"cds_start": 1354,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047447358.1",
"gene_hgnc_id": 17008,
"gene_symbol": "TOPBP1",
"hgvs_c": "c.1354A>C",
"hgvs_p": "p.Lys452Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047303314.1",
"strand": false,
"transcript": "XM_047447358.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 632,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3400,
"cdna_start": null,
"cds_end": null,
"cds_length": 1899,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000933451.1",
"gene_hgnc_id": 17008,
"gene_symbol": "TOPBP1",
"hgvs_c": "c.922+3827A>C",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603510.1",
"strand": false,
"transcript": "ENST00000933451.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 811,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000509162.1",
"gene_hgnc_id": 17008,
"gene_symbol": "TOPBP1",
"hgvs_c": "n.425A>C",
"hgvs_p": null,
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000509162.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
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"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1142,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000511439.5",
"gene_hgnc_id": 17008,
"gene_symbol": "TOPBP1",
"hgvs_c": "n.740A>C",
"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": "ENST00000511439.5",
"transcript_support_level": 5
},
{
"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": 402,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000572787.1",
"gene_hgnc_id": 17008,
"gene_symbol": "TOPBP1",
"hgvs_c": "n.*336A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000458790.1",
"strand": true,
"transcript": "ENST00000572787.1",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs3192149",
"effect": "missense_variant",
"frequency_reference_population": 0.7437685,
"gene_hgnc_id": 17008,
"gene_symbol": "TOPBP1",
"gnomad_exomes_ac": 1087448,
"gnomad_exomes_af": 0.744035,
"gnomad_exomes_homalt": 406496,
"gnomad_genomes_ac": 112682,
"gnomad_genomes_af": 0.741202,
"gnomad_genomes_homalt": 42049,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 448545,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.532,
"pos": 133649518,
"ref": "T",
"revel_prediction": "Benign",
"revel_score": 0.098,
"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_007027.4"
}
]
}