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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: 19-5785652-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=5785652&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3"
],
"effects": [
"missense_variant"
],
"gene_symbol": "DUS3L",
"hgnc_id": 26920,
"hgvs_c": "c.1702G>A",
"hgvs_p": "p.Val568Met",
"inheritance_mode": "AR",
"pathogenic_score": 3,
"score": 3,
"transcript": "NM_020175.3",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3"
],
"effects": [
"upstream_gene_variant"
],
"gene_symbol": "ENSG00000267157",
"hgnc_id": null,
"hgvs_c": "c.-33G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 3,
"score": 3,
"transcript": "ENST00000586012.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_score": 3,
"allele_count_reference_population": 103,
"alphamissense_prediction": null,
"alphamissense_score": 0.4443,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.12,
"chr": "19",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8290757536888123,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 650,
"aa_ref": "V",
"aa_start": 568,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2038,
"cdna_start": 1724,
"cds_end": null,
"cds_length": 1953,
"cds_start": 1702,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_020175.3",
"gene_hgnc_id": 26920,
"gene_symbol": "DUS3L",
"hgvs_c": "c.1702G>A",
"hgvs_p": "p.Val568Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000309061.12",
"protein_coding": true,
"protein_id": "NP_064560.2",
"strand": false,
"transcript": "NM_020175.3",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 650,
"aa_ref": "V",
"aa_start": 568,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2038,
"cdna_start": 1724,
"cds_end": null,
"cds_length": 1953,
"cds_start": 1702,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000309061.12",
"gene_hgnc_id": 26920,
"gene_symbol": "DUS3L",
"hgvs_c": "c.1702G>A",
"hgvs_p": "p.Val568Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_020175.3",
"protein_coding": true,
"protein_id": "ENSP00000311977.5",
"strand": false,
"transcript": "ENST00000309061.12",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 408,
"aa_ref": "V",
"aa_start": 326,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1355,
"cdna_start": 1041,
"cds_end": null,
"cds_length": 1227,
"cds_start": 976,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000320699.12",
"gene_hgnc_id": 26920,
"gene_symbol": "DUS3L",
"hgvs_c": "c.976G>A",
"hgvs_p": "p.Val326Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000315558.7",
"strand": false,
"transcript": "ENST00000320699.12",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 663,
"aa_ref": "V",
"aa_start": 581,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2090,
"cdna_start": 1776,
"cds_end": null,
"cds_length": 1992,
"cds_start": 1741,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000931382.1",
"gene_hgnc_id": 26920,
"gene_symbol": "DUS3L",
"hgvs_c": "c.1741G>A",
"hgvs_p": "p.Val581Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601441.1",
"strand": false,
"transcript": "ENST00000931382.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 656,
"aa_ref": "V",
"aa_start": 574,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2066,
"cdna_start": 1752,
"cds_end": null,
"cds_length": 1971,
"cds_start": 1720,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000931383.1",
"gene_hgnc_id": 26920,
"gene_symbol": "DUS3L",
"hgvs_c": "c.1720G>A",
"hgvs_p": "p.Val574Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601442.1",
"strand": false,
"transcript": "ENST00000931383.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 642,
"aa_ref": "V",
"aa_start": 560,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2017,
"cdna_start": 1707,
"cds_end": null,
"cds_length": 1929,
"cds_start": 1678,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000880234.1",
"gene_hgnc_id": 26920,
"gene_symbol": "DUS3L",
"hgvs_c": "c.1678G>A",
"hgvs_p": "p.Val560Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000550293.1",
"strand": false,
"transcript": "ENST00000880234.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 638,
"aa_ref": "V",
"aa_start": 556,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1997,
"cdna_start": 1688,
"cds_end": null,
"cds_length": 1917,
"cds_start": 1666,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000880235.1",
"gene_hgnc_id": 26920,
"gene_symbol": "DUS3L",
"hgvs_c": "c.1666G>A",
"hgvs_p": "p.Val556Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000550294.1",
"strand": false,
"transcript": "ENST00000880235.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 636,
"aa_ref": "V",
"aa_start": 554,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2041,
"cdna_start": 1724,
"cds_end": null,
"cds_length": 1911,
"cds_start": 1660,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000958714.1",
"gene_hgnc_id": 26920,
"gene_symbol": "DUS3L",
"hgvs_c": "c.1660G>A",
"hgvs_p": "p.Val554Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000628773.1",
"strand": false,
"transcript": "ENST00000958714.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 408,
"aa_ref": "V",
"aa_start": 326,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1312,
"cdna_start": 998,
"cds_end": null,
"cds_length": 1227,
"cds_start": 976,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001161619.2",
"gene_hgnc_id": 26920,
"gene_symbol": "DUS3L",
"hgvs_c": "c.976G>A",
"hgvs_p": "p.Val326Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001155091.1",
"strand": false,
"transcript": "NM_001161619.2",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 168,
"aa_ref": "V",
"aa_start": 35,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 833,
"cdna_start": 104,
"cds_end": null,
"cds_length": 507,
"cds_start": 103,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000590343.1",
"gene_hgnc_id": 26920,
"gene_symbol": "DUS3L",
"hgvs_c": "c.103G>A",
"hgvs_p": "p.Val35Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000466351.1",
"strand": false,
"transcript": "ENST00000590343.1",
"transcript_support_level": 2
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 636,
"aa_ref": "V",
"aa_start": 554,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1996,
"cdna_start": 1682,
"cds_end": null,
"cds_length": 1911,
"cds_start": 1660,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_017027020.2",
"gene_hgnc_id": 26920,
"gene_symbol": "DUS3L",
"hgvs_c": "c.1660G>A",
"hgvs_p": "p.Val554Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016882509.1",
"strand": false,
"transcript": "XM_017027020.2",
"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": 2301,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000589085.5",
"gene_hgnc_id": 26920,
"gene_symbol": "DUS3L",
"hgvs_c": "n.1987G>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": "ENST00000589085.5",
"transcript_support_level": 5
},
{
"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": 453,
"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": "ENST00000589841.5",
"gene_hgnc_id": 26920,
"gene_symbol": "DUS3L",
"hgvs_c": "n.348G>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": "ENST00000589841.5",
"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": 768,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000591560.5",
"gene_hgnc_id": 26920,
"gene_symbol": "DUS3L",
"hgvs_c": "n.*147G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000467987.1",
"strand": false,
"transcript": "ENST00000591560.5",
"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": 797,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000592468.5",
"gene_hgnc_id": 26920,
"gene_symbol": "DUS3L",
"hgvs_c": "n.*273G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000468075.1",
"strand": false,
"transcript": "ENST00000592468.5",
"transcript_support_level": 5
},
{
"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": 701,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000592673.1",
"gene_hgnc_id": 26920,
"gene_symbol": "DUS3L",
"hgvs_c": "n.604G>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": "ENST00000592673.1",
"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": 768,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000591560.5",
"gene_hgnc_id": 26920,
"gene_symbol": "DUS3L",
"hgvs_c": "n.*147G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000467987.1",
"strand": false,
"transcript": "ENST00000591560.5",
"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": 797,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000592468.5",
"gene_hgnc_id": 26920,
"gene_symbol": "DUS3L",
"hgvs_c": "n.*273G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000468075.1",
"strand": false,
"transcript": "ENST00000592468.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 77,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 581,
"cdna_start": null,
"cds_end": null,
"cds_length": 234,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000586012.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000267157",
"hgvs_c": "c.-33G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000466514.1",
"strand": true,
"transcript": "ENST00000586012.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 485,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1512,
"cdna_start": null,
"cds_end": null,
"cds_length": 1458,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 10,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047439111.1",
"gene_hgnc_id": 26920,
"gene_symbol": "DUS3L",
"hgvs_c": "c.*147G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047295067.1",
"strand": true,
"transcript": "XM_047439111.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs141670860",
"effect": "missense_variant",
"frequency_reference_population": 0.00006388738,
"gene_hgnc_id": 26920,
"gene_symbol": "DUS3L",
"gnomad_exomes_ac": 98,
"gnomad_exomes_af": 0.0000671253,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 5,
"gnomad_genomes_af": 0.0000328394,
"gnomad_genomes_homalt": 0,
"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": "Uncertain_significance",
"phylop100way_score": 5.717,
"pos": 5785652,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.33,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_020175.3"
}
]
}