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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: 19-7529166-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=7529166&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 19,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "MCOLN1",
"hgnc_id": 13356,
"hgvs_c": "c.1200C>T",
"hgvs_p": "p.Gly400Gly",
"inheritance_mode": "AR,AD",
"pathogenic_score": 0,
"score": -19,
"transcript": "NM_020533.3",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_score": -19,
"allele_count_reference_population": 5475,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.26,
"chr": "19",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": "Mucolipidosis type IV,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.25999999046325684,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 580,
"aa_ref": "G",
"aa_start": 400,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2084,
"cdna_start": 1327,
"cds_end": null,
"cds_length": 1743,
"cds_start": 1200,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_020533.3",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1200C>T",
"hgvs_p": "p.Gly400Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000264079.11",
"protein_coding": true,
"protein_id": "NP_065394.1",
"strand": true,
"transcript": "NM_020533.3",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 580,
"aa_ref": "G",
"aa_start": 400,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2084,
"cdna_start": 1327,
"cds_end": null,
"cds_length": 1743,
"cds_start": 1200,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000264079.11",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1200C>T",
"hgvs_p": "p.Gly400Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_020533.3",
"protein_coding": true,
"protein_id": "ENSP00000264079.5",
"strand": true,
"transcript": "ENST00000264079.11",
"transcript_support_level": 1
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 636,
"aa_ref": "G",
"aa_start": 456,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2242,
"cdna_start": 1504,
"cds_end": null,
"cds_length": 1911,
"cds_start": 1368,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000852002.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1368C>T",
"hgvs_p": "p.Gly456Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000522061.1",
"strand": true,
"transcript": "ENST00000852002.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 631,
"aa_ref": "G",
"aa_start": 400,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2216,
"cdna_start": 1325,
"cds_end": null,
"cds_length": 1896,
"cds_start": 1200,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000915843.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1200C>T",
"hgvs_p": "p.Gly400Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000585902.1",
"strand": true,
"transcript": "ENST00000915843.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 591,
"aa_ref": "G",
"aa_start": 411,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2097,
"cdna_start": 1340,
"cds_end": null,
"cds_length": 1776,
"cds_start": 1233,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000915842.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1233C>T",
"hgvs_p": "p.Gly411Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000585901.1",
"strand": true,
"transcript": "ENST00000915842.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 586,
"aa_ref": "G",
"aa_start": 406,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2115,
"cdna_start": 1358,
"cds_end": null,
"cds_length": 1761,
"cds_start": 1218,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000852000.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1218C>T",
"hgvs_p": "p.Gly406Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000522059.1",
"strand": true,
"transcript": "ENST00000852000.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 586,
"aa_ref": "G",
"aa_start": 406,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2055,
"cdna_start": 1325,
"cds_end": null,
"cds_length": 1761,
"cds_start": 1218,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000852006.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1218C>T",
"hgvs_p": "p.Gly406Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000522065.1",
"strand": true,
"transcript": "ENST00000852006.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 578,
"aa_ref": "G",
"aa_start": 398,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2052,
"cdna_start": 1314,
"cds_end": null,
"cds_length": 1737,
"cds_start": 1194,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000852003.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1194C>T",
"hgvs_p": "p.Gly398Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000522062.1",
"strand": true,
"transcript": "ENST00000852003.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 552,
"aa_ref": "G",
"aa_start": 400,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2013,
"cdna_start": 1340,
"cds_end": null,
"cds_length": 1659,
"cds_start": 1200,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000852001.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1200C>T",
"hgvs_p": "p.Gly400Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000522060.1",
"strand": true,
"transcript": "ENST00000852001.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 539,
"aa_ref": "G",
"aa_start": 400,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1935,
"cdna_start": 1320,
"cds_end": null,
"cds_length": 1620,
"cds_start": 1200,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000852004.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1200C>T",
"hgvs_p": "p.Gly400Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000522063.1",
"strand": true,
"transcript": "ENST00000852004.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 499,
"aa_ref": "G",
"aa_start": 319,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1767,
"cdna_start": 1029,
"cds_end": null,
"cds_length": 1500,
"cds_start": 957,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000915844.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.957C>T",
"hgvs_p": "p.Gly319Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000585903.1",
"strand": true,
"transcript": "ENST00000915844.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 484,
"aa_ref": "G",
"aa_start": 304,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1766,
"cdna_start": 1039,
"cds_end": null,
"cds_length": 1455,
"cds_start": 912,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000852005.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.912C>T",
"hgvs_p": "p.Gly304Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000522064.1",
"strand": true,
"transcript": "ENST00000852005.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 478,
"aa_ref": "G",
"aa_start": 298,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1738,
"cdna_start": 999,
"cds_end": null,
"cds_length": 1437,
"cds_start": 894,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000948925.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.894C>T",
"hgvs_p": "p.Gly298Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000618984.1",
"strand": true,
"transcript": "ENST00000948925.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 181,
"aa_ref": "G",
"aa_start": 25,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 666,
"cdna_start": 77,
"cds_end": null,
"cds_length": 546,
"cds_start": 75,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000599334.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.75C>T",
"hgvs_p": "p.Gly25Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000472176.1",
"strand": true,
"transcript": "ENST00000599334.1",
"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": 2253,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000394321.9",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "n.1515C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000394321.9",
"transcript_support_level": 2
},
{
"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": 470,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000594692.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "n.196C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000594692.1",
"transcript_support_level": 3
},
{
"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": 758,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000595860.5",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "n.383C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000595860.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs28541364",
"effect": "synonymous_variant",
"frequency_reference_population": 0.0033929376,
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"gnomad_exomes_ac": 3473,
"gnomad_exomes_af": 0.00237655,
"gnomad_exomes_homalt": 71,
"gnomad_genomes_ac": 2002,
"gnomad_genomes_af": 0.0131463,
"gnomad_genomes_homalt": 38,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 109,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "Mucolipidosis type IV|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -1.169,
"pos": 7529166,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.10999999940395355,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.11,
"transcript": "NM_020533.3"
}
]
}