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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: 17-18277723-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=18277723&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "TOP3A",
"hgnc_id": 11992,
"hgvs_c": "c.2779G>A",
"hgvs_p": "p.Glu927Lys",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_004618.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 8,
"alphamissense_prediction": null,
"alphamissense_score": 0.172,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.31,
"chr": "17",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.4499968886375427,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1001,
"aa_ref": "E",
"aa_start": 927,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6596,
"cdna_start": 2995,
"cds_end": null,
"cds_length": 3006,
"cds_start": 2779,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_004618.5",
"gene_hgnc_id": 11992,
"gene_symbol": "TOP3A",
"hgvs_c": "c.2779G>A",
"hgvs_p": "p.Glu927Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000321105.10",
"protein_coding": true,
"protein_id": "NP_004609.1",
"strand": false,
"transcript": "NM_004618.5",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1001,
"aa_ref": "E",
"aa_start": 927,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6596,
"cdna_start": 2995,
"cds_end": null,
"cds_length": 3006,
"cds_start": 2779,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000321105.10",
"gene_hgnc_id": 11992,
"gene_symbol": "TOP3A",
"hgvs_c": "c.2779G>A",
"hgvs_p": "p.Glu927Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004618.5",
"protein_coding": true,
"protein_id": "ENSP00000321636.5",
"strand": false,
"transcript": "ENST00000321105.10",
"transcript_support_level": 1
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 975,
"aa_ref": "E",
"aa_start": 902,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2929,
"cdna_start": 2704,
"cds_end": null,
"cds_length": 2929,
"cds_start": 2704,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000580095.5",
"gene_hgnc_id": 11992,
"gene_symbol": "TOP3A",
"hgvs_c": "c.2704G>A",
"hgvs_p": "p.Glu902Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000462790.1",
"strand": false,
"transcript": "ENST00000580095.5",
"transcript_support_level": 1
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1053,
"aa_ref": "E",
"aa_start": 979,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4243,
"cdna_start": 3137,
"cds_end": null,
"cds_length": 3162,
"cds_start": 2935,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000924978.1",
"gene_hgnc_id": 11992,
"gene_symbol": "TOP3A",
"hgvs_c": "c.2935G>A",
"hgvs_p": "p.Glu979Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595037.1",
"strand": false,
"transcript": "ENST00000924978.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 976,
"aa_ref": "E",
"aa_start": 902,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4271,
"cdna_start": 2901,
"cds_end": null,
"cds_length": 2931,
"cds_start": 2704,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000924977.1",
"gene_hgnc_id": 11992,
"gene_symbol": "TOP3A",
"hgvs_c": "c.2704G>A",
"hgvs_p": "p.Glu902Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595036.1",
"strand": false,
"transcript": "ENST00000924977.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 963,
"aa_ref": "E",
"aa_start": 889,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3648,
"cdna_start": 2848,
"cds_end": null,
"cds_length": 2892,
"cds_start": 2665,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000947450.1",
"gene_hgnc_id": 11992,
"gene_symbol": "TOP3A",
"hgvs_c": "c.2665G>A",
"hgvs_p": "p.Glu889Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000617509.1",
"strand": false,
"transcript": "ENST00000947450.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 951,
"aa_ref": "E",
"aa_start": 877,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3633,
"cdna_start": 2823,
"cds_end": null,
"cds_length": 2856,
"cds_start": 2629,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000924980.1",
"gene_hgnc_id": 11992,
"gene_symbol": "TOP3A",
"hgvs_c": "c.2629G>A",
"hgvs_p": "p.Glu877Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595039.1",
"strand": false,
"transcript": "ENST00000924980.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 906,
"aa_ref": "E",
"aa_start": 832,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6522,
"cdna_start": 2921,
"cds_end": null,
"cds_length": 2721,
"cds_start": 2494,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_001320759.2",
"gene_hgnc_id": 11992,
"gene_symbol": "TOP3A",
"hgvs_c": "c.2494G>A",
"hgvs_p": "p.Glu832Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001307688.1",
"strand": false,
"transcript": "NM_001320759.2",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 733,
"aa_ref": "E",
"aa_start": 659,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3259,
"cdna_start": 2160,
"cds_end": null,
"cds_length": 2202,
"cds_start": 1975,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000924979.1",
"gene_hgnc_id": 11992,
"gene_symbol": "TOP3A",
"hgvs_c": "c.1975G>A",
"hgvs_p": "p.Glu659Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595038.1",
"strand": false,
"transcript": "ENST00000924979.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 694,
"aa_ref": "E",
"aa_start": 620,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6089,
"cdna_start": 2488,
"cds_end": null,
"cds_length": 2085,
"cds_start": 1858,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "XM_047436633.1",
"gene_hgnc_id": 11992,
"gene_symbol": "TOP3A",
"hgvs_c": "c.1858G>A",
"hgvs_p": "p.Glu620Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047292589.1",
"strand": false,
"transcript": "XM_047436633.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 694,
"aa_ref": "E",
"aa_start": 620,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6155,
"cdna_start": 2554,
"cds_end": null,
"cds_length": 2085,
"cds_start": 1858,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "XM_047436634.1",
"gene_hgnc_id": 11992,
"gene_symbol": "TOP3A",
"hgvs_c": "c.1858G>A",
"hgvs_p": "p.Glu620Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047292590.1",
"strand": false,
"transcript": "XM_047436634.1",
"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": 3196,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000469739.6",
"gene_hgnc_id": 11992,
"gene_symbol": "TOP3A",
"hgvs_c": "n.2134G>A",
"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": "ENST00000469739.6",
"transcript_support_level": 2
},
{
"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": 3239,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 18,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000582981.5",
"gene_hgnc_id": 11992,
"gene_symbol": "TOP3A",
"hgvs_c": "n.*2435G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000462378.1",
"strand": false,
"transcript": "ENST00000582981.5",
"transcript_support_level": 2
},
{
"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": 3661,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000584582.5",
"gene_hgnc_id": 11992,
"gene_symbol": "TOP3A",
"hgvs_c": "n.*2435G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000462136.1",
"strand": false,
"transcript": "ENST00000584582.5",
"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": 3239,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 18,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000582981.5",
"gene_hgnc_id": 11992,
"gene_symbol": "TOP3A",
"hgvs_c": "n.*2435G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000462378.1",
"strand": false,
"transcript": "ENST00000582981.5",
"transcript_support_level": 2
},
{
"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": 3661,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000584582.5",
"gene_hgnc_id": 11992,
"gene_symbol": "TOP3A",
"hgvs_c": "n.*2435G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000462136.1",
"strand": false,
"transcript": "ENST00000584582.5",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs578143841",
"effect": "missense_variant",
"frequency_reference_population": 0.000005473686,
"gene_hgnc_id": 11992,
"gene_symbol": "TOP3A",
"gnomad_exomes_ac": 8,
"gnomad_exomes_af": 0.00000547369,
"gnomad_exomes_homalt": 0,
"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": null,
"phenotype_combined": null,
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 7.509,
"pos": 18277723,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.137,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_004618.5"
}
]
}