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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: 19-7528920-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=7528920&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 7528920,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_020533.3",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.1084G>A",
"hgvs_p": "p.Asp362Asn",
"transcript": "NM_020533.3",
"protein_id": "NP_065394.1",
"transcript_support_level": null,
"aa_start": 362,
"aa_end": null,
"aa_length": 580,
"cds_start": 1084,
"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": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.1084G>A",
"hgvs_p": "p.Asp362Asn",
"transcript": "ENST00000264079.11",
"protein_id": "ENSP00000264079.5",
"transcript_support_level": 1,
"aa_start": 362,
"aa_end": null,
"aa_length": 580,
"cds_start": 1084,
"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": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.1252G>A",
"hgvs_p": "p.Asp418Asn",
"transcript": "ENST00000852002.1",
"protein_id": "ENSP00000522061.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 636,
"cds_start": 1252,
"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": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.1084G>A",
"hgvs_p": "p.Asp362Asn",
"transcript": "ENST00000915843.1",
"protein_id": "ENSP00000585902.1",
"transcript_support_level": null,
"aa_start": 362,
"aa_end": null,
"aa_length": 631,
"cds_start": 1084,
"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": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.1117G>A",
"hgvs_p": "p.Asp373Asn",
"transcript": "ENST00000915842.1",
"protein_id": "ENSP00000585901.1",
"transcript_support_level": null,
"aa_start": 373,
"aa_end": null,
"aa_length": 591,
"cds_start": 1117,
"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": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.1102G>A",
"hgvs_p": "p.Asp368Asn",
"transcript": "ENST00000852000.1",
"protein_id": "ENSP00000522059.1",
"transcript_support_level": null,
"aa_start": 368,
"aa_end": null,
"aa_length": 586,
"cds_start": 1102,
"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": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.1102G>A",
"hgvs_p": "p.Asp368Asn",
"transcript": "ENST00000852006.1",
"protein_id": "ENSP00000522065.1",
"transcript_support_level": null,
"aa_start": 368,
"aa_end": null,
"aa_length": 586,
"cds_start": 1102,
"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": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.1078G>A",
"hgvs_p": "p.Asp360Asn",
"transcript": "ENST00000852003.1",
"protein_id": "ENSP00000522062.1",
"transcript_support_level": null,
"aa_start": 360,
"aa_end": null,
"aa_length": 578,
"cds_start": 1078,
"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": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.1084G>A",
"hgvs_p": "p.Asp362Asn",
"transcript": "ENST00000852001.1",
"protein_id": "ENSP00000522060.1",
"transcript_support_level": null,
"aa_start": 362,
"aa_end": null,
"aa_length": 552,
"cds_start": 1084,
"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": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.1084G>A",
"hgvs_p": "p.Asp362Asn",
"transcript": "ENST00000852004.1",
"protein_id": "ENSP00000522063.1",
"transcript_support_level": null,
"aa_start": 362,
"aa_end": null,
"aa_length": 539,
"cds_start": 1084,
"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": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.841G>A",
"hgvs_p": "p.Asp281Asn",
"transcript": "ENST00000915844.1",
"protein_id": "ENSP00000585903.1",
"transcript_support_level": null,
"aa_start": 281,
"aa_end": null,
"aa_length": 499,
"cds_start": 841,
"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": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.796G>A",
"hgvs_p": "p.Asp266Asn",
"transcript": "ENST00000852005.1",
"protein_id": "ENSP00000522064.1",
"transcript_support_level": null,
"aa_start": 266,
"aa_end": null,
"aa_length": 484,
"cds_start": 796,
"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": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.778G>A",
"hgvs_p": "p.Asp260Asn",
"transcript": "ENST00000948925.1",
"protein_id": "ENSP00000618984.1",
"transcript_support_level": null,
"aa_start": 260,
"aa_end": null,
"aa_length": 478,
"cds_start": 778,
"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": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "n.1399G>A",
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "n.267G>A",
"hgvs_p": null,
"transcript": "ENST00000595860.5",
"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": "ENST00000595860.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "c.-42G>A",
"hgvs_p": null,
"transcript": "ENST00000599334.1",
"protein_id": "ENSP00000472176.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 181,
"cds_start": null,
"cds_end": null,
"cds_length": 546,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000599334.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"hgvs_c": "n.-51G>A",
"hgvs_p": null,
"transcript": "ENST00000594692.1",
"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": "ENST00000594692.1"
}
],
"gene_symbol": "MCOLN1",
"gene_hgnc_id": 13356,
"dbsnp": "rs121908372",
"frequency_reference_population": 0.000005472533,
"hom_count_reference_population": 0,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.00000547253,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9848328232765198,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.606,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.96,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.1,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.602,
"phylop100way_prediction": "Pathogenic",
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM5,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM5",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_020533.3",
"gene_symbol": "MCOLN1",
"hgnc_id": 13356,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1084G>A",
"hgvs_p": "p.Asp362Asn"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}