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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: 19-7533560-AG-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=7533560&ref=AG&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PS3",
"PM2",
"PP5_Moderate"
],
"effects": [
"frameshift_variant"
],
"gene_symbol": "MCOLN1",
"hgnc_id": 13356,
"hgvs_c": "c.1615delG",
"hgvs_p": "p.Ala539fs",
"inheritance_mode": "AR,AD",
"pathogenic_score": 16,
"score": 16,
"transcript": "NM_020533.3",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PS3",
"PM2",
"PP5_Moderate"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "ENSG00000305109",
"hgnc_id": null,
"hgvs_c": "n.2023delC",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 8,
"score": 8,
"transcript": "ENST00000808821.1",
"verdict": "Likely_pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PS3",
"PM2",
"PP5_Moderate"
],
"effects": [
"upstream_gene_variant"
],
"gene_symbol": "ENSG00000268614",
"hgnc_id": null,
"hgvs_c": "n.-35delG",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 8,
"score": 8,
"transcript": "ENST00000601870.1",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PS3,PM2,PP5_Moderate",
"acmg_score": 16,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "19",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Mucolipidosis type IV",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1 O:1",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 580,
"aa_ref": "A",
"aa_start": 539,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2084,
"cdna_start": 1742,
"cds_end": null,
"cds_length": 1743,
"cds_start": 1615,
"consequences": [
"frameshift_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_020533.3",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1615delG",
"hgvs_p": "p.Ala539fs",
"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": null,
"aa_end": null,
"aa_length": 580,
"aa_ref": "A",
"aa_start": 539,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2084,
"cdna_start": 1742,
"cds_end": null,
"cds_length": 1743,
"cds_start": 1615,
"consequences": [
"frameshift_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000264079.11",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1615delG",
"hgvs_p": "p.Ala539fs",
"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": null,
"aa_end": null,
"aa_length": 636,
"aa_ref": "A",
"aa_start": 595,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2242,
"cdna_start": 1919,
"cds_end": null,
"cds_length": 1911,
"cds_start": 1783,
"consequences": [
"frameshift_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000852002.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1783delG",
"hgvs_p": "p.Ala595fs",
"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": null,
"aa_end": null,
"aa_length": 631,
"aa_ref": "A",
"aa_start": 590,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2216,
"cdna_start": 1893,
"cds_end": null,
"cds_length": 1896,
"cds_start": 1768,
"consequences": [
"frameshift_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000915843.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1768delG",
"hgvs_p": "p.Ala590fs",
"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": null,
"aa_end": null,
"aa_length": 591,
"aa_ref": "A",
"aa_start": 550,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2097,
"cdna_start": 1755,
"cds_end": null,
"cds_length": 1776,
"cds_start": 1648,
"consequences": [
"frameshift_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000915842.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1648delG",
"hgvs_p": "p.Ala550fs",
"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": null,
"aa_end": null,
"aa_length": 586,
"aa_ref": "A",
"aa_start": 545,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2115,
"cdna_start": 1773,
"cds_end": null,
"cds_length": 1761,
"cds_start": 1633,
"consequences": [
"frameshift_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000852000.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1633delG",
"hgvs_p": "p.Ala545fs",
"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": null,
"aa_end": null,
"aa_length": 586,
"aa_ref": "A",
"aa_start": 545,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2055,
"cdna_start": 1740,
"cds_end": null,
"cds_length": 1761,
"cds_start": 1633,
"consequences": [
"frameshift_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000852006.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1633delG",
"hgvs_p": "p.Ala545fs",
"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": null,
"aa_end": null,
"aa_length": 578,
"aa_ref": "A",
"aa_start": 537,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2052,
"cdna_start": 1729,
"cds_end": null,
"cds_length": 1737,
"cds_start": 1609,
"consequences": [
"frameshift_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000852003.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1609delG",
"hgvs_p": "p.Ala537fs",
"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": null,
"aa_end": null,
"aa_length": 552,
"aa_ref": "A",
"aa_start": 511,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2013,
"cdna_start": 1671,
"cds_end": null,
"cds_length": 1659,
"cds_start": 1531,
"consequences": [
"frameshift_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000852001.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1531delG",
"hgvs_p": "p.Ala511fs",
"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": null,
"aa_end": null,
"aa_length": 539,
"aa_ref": "A",
"aa_start": 498,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1935,
"cdna_start": 1612,
"cds_end": null,
"cds_length": 1620,
"cds_start": 1492,
"consequences": [
"frameshift_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000852004.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1492delG",
"hgvs_p": "p.Ala498fs",
"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": null,
"aa_end": null,
"aa_length": 499,
"aa_ref": "A",
"aa_start": 458,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1767,
"cdna_start": 1444,
"cds_end": null,
"cds_length": 1500,
"cds_start": 1372,
"consequences": [
"frameshift_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000915844.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1372delG",
"hgvs_p": "p.Ala458fs",
"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": null,
"aa_end": null,
"aa_length": 484,
"aa_ref": "A",
"aa_start": 443,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1766,
"cdna_start": 1454,
"cds_end": null,
"cds_length": 1455,
"cds_start": 1327,
"consequences": [
"frameshift_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000852005.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1327delG",
"hgvs_p": "p.Ala443fs",
"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": null,
"aa_end": null,
"aa_length": 478,
"aa_ref": "A",
"aa_start": 437,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1738,
"cdna_start": 1414,
"cds_end": null,
"cds_length": 1437,
"cds_start": 1309,
"consequences": [
"frameshift_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000948925.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.1309delG",
"hgvs_p": "p.Ala437fs",
"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": null,
"aa_end": null,
"aa_length": 181,
"aa_ref": "G",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 666,
"cdna_start": 343,
"cds_end": null,
"cds_length": 546,
"cds_start": 341,
"consequences": [
"frameshift_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000599334.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "c.341delG",
"hgvs_p": "p.Gly114fs",
"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": 12,
"exon_rank_end": null,
"feature": "ENST00000394321.9",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "n.1930delG",
"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": 492,
"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": "ENST00000602227.1",
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"hgvs_c": "n.169delG",
"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": "ENST00000602227.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2857,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000808821.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000305109",
"hgvs_c": "n.2023delC",
"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": "ENST00000808821.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 942,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 10,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000601870.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000268614",
"hgvs_c": "n.-35delG",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000471492.1",
"strand": true,
"transcript": "ENST00000601870.1",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1555742780",
"effect": "frameshift_variant",
"frequency_reference_population": 6.850028e-7,
"gene_hgnc_id": 13356,
"gene_symbol": "MCOLN1",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.85003e-7,
"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": "Pathogenic",
"phenotype_combined": "Mucolipidosis type IV",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.219,
"pos": 7533560,
"ref": "AG",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_020533.3"
}
]
}