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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: 12-101765291-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=101765291&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 101765291,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_024312.5",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"hgvs_c": "c.1626A>G",
"hgvs_p": "p.Glu542Glu",
"transcript": "NM_024312.5",
"protein_id": "NP_077288.2",
"transcript_support_level": null,
"aa_start": 542,
"aa_end": null,
"aa_length": 1256,
"cds_start": 1626,
"cds_end": null,
"cds_length": 3771,
"cdna_start": 1910,
"cdna_end": null,
"cdna_length": 5720,
"mane_select": "ENST00000299314.12",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024312.5"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"hgvs_c": "c.1626A>G",
"hgvs_p": "p.Glu542Glu",
"transcript": "ENST00000299314.12",
"protein_id": "ENSP00000299314.7",
"transcript_support_level": 1,
"aa_start": 542,
"aa_end": null,
"aa_length": 1256,
"cds_start": 1626,
"cds_end": null,
"cds_length": 3771,
"cdna_start": 1910,
"cdna_end": null,
"cdna_length": 5720,
"mane_select": "NM_024312.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000299314.12"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"hgvs_c": "c.1647A>G",
"hgvs_p": "p.Glu549Glu",
"transcript": "ENST00000917136.1",
"protein_id": "ENSP00000587195.1",
"transcript_support_level": null,
"aa_start": 549,
"aa_end": null,
"aa_length": 1263,
"cds_start": 1647,
"cds_end": null,
"cds_length": 3792,
"cdna_start": 1840,
"cdna_end": null,
"cdna_length": 5647,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917136.1"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"hgvs_c": "c.1620A>G",
"hgvs_p": "p.Glu540Glu",
"transcript": "ENST00000917134.1",
"protein_id": "ENSP00000587193.1",
"transcript_support_level": null,
"aa_start": 540,
"aa_end": null,
"aa_length": 1254,
"cds_start": 1620,
"cds_end": null,
"cds_length": 3765,
"cdna_start": 1891,
"cdna_end": null,
"cdna_length": 5703,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917134.1"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"hgvs_c": "c.1506A>G",
"hgvs_p": "p.Glu502Glu",
"transcript": "ENST00000917133.1",
"protein_id": "ENSP00000587192.1",
"transcript_support_level": null,
"aa_start": 502,
"aa_end": null,
"aa_length": 1216,
"cds_start": 1506,
"cds_end": null,
"cds_length": 3651,
"cdna_start": 1810,
"cdna_end": null,
"cdna_length": 5633,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917133.1"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"hgvs_c": "c.1473A>G",
"hgvs_p": "p.Glu491Glu",
"transcript": "ENST00000917135.1",
"protein_id": "ENSP00000587194.1",
"transcript_support_level": null,
"aa_start": 491,
"aa_end": null,
"aa_length": 1205,
"cds_start": 1473,
"cds_end": null,
"cds_length": 3618,
"cdna_start": 1738,
"cdna_end": null,
"cdna_length": 5550,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917135.1"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"hgvs_c": "c.1422A>G",
"hgvs_p": "p.Glu474Glu",
"transcript": "ENST00000953730.1",
"protein_id": "ENSP00000623789.1",
"transcript_support_level": null,
"aa_start": 474,
"aa_end": null,
"aa_length": 1188,
"cds_start": 1422,
"cds_end": null,
"cds_length": 3567,
"cdna_start": 1727,
"cdna_end": null,
"cdna_length": 4813,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953730.1"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"hgvs_c": "c.1545A>G",
"hgvs_p": "p.Glu515Glu",
"transcript": "XM_011538731.3",
"protein_id": "XP_011537033.1",
"transcript_support_level": null,
"aa_start": 515,
"aa_end": null,
"aa_length": 1229,
"cds_start": 1545,
"cds_end": null,
"cds_length": 3690,
"cdna_start": 1561,
"cdna_end": null,
"cdna_length": 5371,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011538731.3"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"hgvs_c": "c.1626A>G",
"hgvs_p": "p.Glu542Glu",
"transcript": "XM_006719593.4",
"protein_id": "XP_006719656.1",
"transcript_support_level": null,
"aa_start": 542,
"aa_end": null,
"aa_length": 1179,
"cds_start": 1626,
"cds_end": null,
"cds_length": 3540,
"cdna_start": 1910,
"cdna_end": null,
"cdna_length": 4070,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006719593.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNU6-101P",
"gene_hgnc_id": 47064,
"hgvs_c": "n.*115A>G",
"hgvs_p": null,
"transcript": "ENST00000410323.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 104,
"mane_select": null,
"mane_plus": null,
"biotype": "snRNA",
"feature": "ENST00000410323.1"
}
],
"gene_symbol": "GNPTAB",
"gene_hgnc_id": 29670,
"dbsnp": "rs61745799",
"frequency_reference_population": 0.0007781177,
"hom_count_reference_population": 12,
"allele_count_reference_population": 1251,
"gnomad_exomes_af": 0.000441802,
"gnomad_genomes_af": 0.00399154,
"gnomad_exomes_ac": 643,
"gnomad_genomes_ac": 608,
"gnomad_exomes_homalt": 9,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5199999809265137,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.52,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.761,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_024312.5",
"gene_symbol": "GNPTAB",
"hgnc_id": 29670,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1626A>G",
"hgvs_p": "p.Glu542Glu"
},
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000410323.1",
"gene_symbol": "RNU6-101P",
"hgnc_id": 47064,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*115A>G",
"hgvs_p": null
}
],
"clinvar_disease": "GNPTAB-related disorder,Mucolipidosis type II,Pseudo-Hurler polydystrophy",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:1",
"phenotype_combined": "Mucolipidosis type II|Pseudo-Hurler polydystrophy|GNPTAB-related disorder|Mucolipidosis type II;Pseudo-Hurler polydystrophy",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}