← Back to variant description
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: 19-7527537-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=7527537&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 7527537,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_020533.3",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.589C>T",
"hgvs_p": "p.Pro197Ser",
"transcript": "NM_020533.3",
"protein_id": "NP_065394.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 580,
"cds_start": 589,
"cds_end": null,
"cds_length": 1743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000264079.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_020533.3"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.589C>T",
"hgvs_p": "p.Pro197Ser",
"transcript": "ENST00000264079.11",
"protein_id": "ENSP00000264079.5",
"transcript_support_level": 1,
"aa_start": 197,
"aa_end": null,
"aa_length": 580,
"cds_start": 589,
"cds_end": null,
"cds_length": 1743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_020533.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264079.11"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.589C>T",
"hgvs_p": "p.Pro197Ser",
"transcript": "ENST00000852002.1",
"protein_id": "ENSP00000522061.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 636,
"cds_start": 589,
"cds_end": null,
"cds_length": 1911,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000852002.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.589C>T",
"hgvs_p": "p.Pro197Ser",
"transcript": "ENST00000915843.1",
"protein_id": "ENSP00000585902.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 631,
"cds_start": 589,
"cds_end": null,
"cds_length": 1896,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000915843.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.589C>T",
"hgvs_p": "p.Pro197Ser",
"transcript": "ENST00000852000.1",
"protein_id": "ENSP00000522059.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 586,
"cds_start": 589,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000852000.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.607C>T",
"hgvs_p": "p.Pro203Ser",
"transcript": "ENST00000852006.1",
"protein_id": "ENSP00000522065.1",
"transcript_support_level": null,
"aa_start": 203,
"aa_end": null,
"aa_length": 586,
"cds_start": 607,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000852006.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.583C>T",
"hgvs_p": "p.Pro195Ser",
"transcript": "ENST00000852003.1",
"protein_id": "ENSP00000522062.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 578,
"cds_start": 583,
"cds_end": null,
"cds_length": 1737,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000852003.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.589C>T",
"hgvs_p": "p.Pro197Ser",
"transcript": "ENST00000852001.1",
"protein_id": "ENSP00000522060.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 552,
"cds_start": 589,
"cds_end": null,
"cds_length": 1659,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000852001.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.589C>T",
"hgvs_p": "p.Pro197Ser",
"transcript": "ENST00000852004.1",
"protein_id": "ENSP00000522063.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 539,
"cds_start": 589,
"cds_end": null,
"cds_length": 1620,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000852004.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.572-185C>T",
"hgvs_p": null,
"transcript": "ENST00000915842.1",
"protein_id": "ENSP00000585901.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 591,
"cds_start": null,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000915842.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.438-327C>T",
"hgvs_p": null,
"transcript": "ENST00000915844.1",
"protein_id": "ENSP00000585903.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 499,
"cds_start": null,
"cds_end": null,
"cds_length": 1500,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000915844.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.571+611C>T",
"hgvs_p": null,
"transcript": "ENST00000852005.1",
"protein_id": "ENSP00000522064.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 484,
"cds_start": null,
"cds_end": null,
"cds_length": 1455,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000852005.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.571+611C>T",
"hgvs_p": null,
"transcript": "ENST00000948925.1",
"protein_id": "ENSP00000618984.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 478,
"cds_start": null,
"cds_end": null,
"cds_length": 1437,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948925.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.572-327C>T",
"hgvs_p": null,
"transcript": "ENST00000601003.1",
"protein_id": "ENSP00000469074.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 199,
"cds_start": null,
"cds_end": null,
"cds_length": 602,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000601003.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "n.669C>T",
"hgvs_p": null,
"transcript": "ENST00000394321.9",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000394321.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "n.410C>T",
"hgvs_p": null,
"transcript": "ENST00000598406.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000598406.1"
}
],
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"dbsnp": "rs145706318",
"frequency_reference_population": 0.00057503453,
"hom_count_reference_population": 2,
"allele_count_reference_population": 883,
"gnomad_exomes_af": 0.000597018,
"gnomad_genomes_af": 0.000374961,
"gnomad_exomes_ac": 826,
"gnomad_genomes_ac": 57,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8565285205841064,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.647,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.343,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.05,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.861,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3_Moderate,BS2",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_020533.3",
"gene_symbol": "MCOLN1",
"hgnc_id": 13356,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.589C>T",
"hgvs_p": "p.Pro197Ser"
}
],
"clinvar_disease": "Inborn genetic diseases,Mucolipidosis type IV,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:4",
"phenotype_combined": "Mucolipidosis type IV|not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}