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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: 13-110186475-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=110186475&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 110186475,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000375820.10",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "c.1807C>T",
"hgvs_p": "p.Pro603Ser",
"transcript": "NM_001845.6",
"protein_id": "NP_001836.3",
"transcript_support_level": null,
"aa_start": 603,
"aa_end": null,
"aa_length": 1669,
"cds_start": 1807,
"cds_end": null,
"cds_length": 5010,
"cdna_start": 1937,
"cdna_end": null,
"cdna_length": 6540,
"mane_select": "ENST00000375820.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "c.1807C>T",
"hgvs_p": "p.Pro603Ser",
"transcript": "ENST00000375820.10",
"protein_id": "ENSP00000364979.4",
"transcript_support_level": 1,
"aa_start": 603,
"aa_end": null,
"aa_length": 1669,
"cds_start": 1807,
"cds_end": null,
"cds_length": 5010,
"cdna_start": 1937,
"cdna_end": null,
"cdna_length": 6540,
"mane_select": "NM_001845.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "c.1807C>T",
"hgvs_p": "p.Pro603Ser",
"transcript": "ENST00000650424.2",
"protein_id": "ENSP00000497477.2",
"transcript_support_level": null,
"aa_start": 603,
"aa_end": null,
"aa_length": 1667,
"cds_start": 1807,
"cds_end": null,
"cds_length": 5004,
"cdna_start": 1937,
"cdna_end": null,
"cdna_length": 6386,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "c.1615C>T",
"hgvs_p": "p.Pro539Ser",
"transcript": "ENST00000615732.3",
"protein_id": "ENSP00000478222.3",
"transcript_support_level": 5,
"aa_start": 539,
"aa_end": null,
"aa_length": 1605,
"cds_start": 1615,
"cds_end": null,
"cds_length": 4818,
"cdna_start": 2237,
"cdna_end": null,
"cdna_length": 6742,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "n.1937C>T",
"hgvs_p": null,
"transcript": "ENST00000649738.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2644,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "n.1807C>T",
"hgvs_p": null,
"transcript": "ENST00000714331.1",
"protein_id": "ENSP00000519607.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6423,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "c.1591+800C>T",
"hgvs_p": null,
"transcript": "ENST00000714330.1",
"protein_id": "ENSP00000519606.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1554,
"cds_start": -4,
"cds_end": null,
"cds_length": 4665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6240,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "n.1728+663C>T",
"hgvs_p": null,
"transcript": "ENST00000714329.1",
"protein_id": "ENSP00000519605.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6371,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"dbsnp": "rs747585517",
"frequency_reference_population": 0.000016731361,
"hom_count_reference_population": 0,
"allele_count_reference_population": 27,
"gnomad_exomes_af": 0.0000164212,
"gnomad_genomes_af": 0.0000197091,
"gnomad_exomes_ac": 24,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7368566989898682,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.728,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.0877,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.06,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 6.928,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PP5",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM1",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000375820.10",
"gene_symbol": "COL4A1",
"hgnc_id": 2202,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1807C>T",
"hgvs_p": "p.Pro603Ser"
}
],
"clinvar_disease": " autosomal dominant, intracerebral, pontine, susceptibility to,Autosomal dominant familial hematuria-retinal arteriolar tortuosity-contractures syndrome,Brain small vessel disease 1 with or without ocular anomalies,Congenital anomaly of kidney and urinary tract,Hemorrhage,Microangiopathy and leukoencephalopathy,Retinal arterial tortuosity,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:3",
"phenotype_combined": "Autosomal dominant familial hematuria-retinal arteriolar tortuosity-contractures syndrome|not provided|Congenital anomaly of kidney and urinary tract|Hemorrhage, intracerebral, susceptibility to;Autosomal dominant familial hematuria-retinal arteriolar tortuosity-contractures syndrome;Microangiopathy and leukoencephalopathy, pontine, autosomal dominant;Brain small vessel disease 1 with or without ocular anomalies;Retinal arterial tortuosity|Brain small vessel disease 1 with or without ocular anomalies",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}