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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: 13-110170583-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=110170583&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 110170583,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000375820.10",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "c.3706G>A",
"hgvs_p": "p.Gly1236Arg",
"transcript": "NM_001845.6",
"protein_id": "NP_001836.3",
"transcript_support_level": null,
"aa_start": 1236,
"aa_end": null,
"aa_length": 1669,
"cds_start": 3706,
"cds_end": null,
"cds_length": 5010,
"cdna_start": 3836,
"cdna_end": null,
"cdna_length": 6540,
"mane_select": "ENST00000375820.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "c.3706G>A",
"hgvs_p": "p.Gly1236Arg",
"transcript": "ENST00000375820.10",
"protein_id": "ENSP00000364979.4",
"transcript_support_level": 1,
"aa_start": 1236,
"aa_end": null,
"aa_length": 1669,
"cds_start": 3706,
"cds_end": null,
"cds_length": 5010,
"cdna_start": 3836,
"cdna_end": null,
"cdna_length": 6540,
"mane_select": "NM_001845.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "c.3706G>A",
"hgvs_p": "p.Gly1236Arg",
"transcript": "ENST00000650424.2",
"protein_id": "ENSP00000497477.2",
"transcript_support_level": null,
"aa_start": 1236,
"aa_end": null,
"aa_length": 1667,
"cds_start": 3706,
"cds_end": null,
"cds_length": 5004,
"cdna_start": 3836,
"cdna_end": null,
"cdna_length": 6386,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "c.3514G>A",
"hgvs_p": "p.Gly1172Arg",
"transcript": "ENST00000615732.3",
"protein_id": "ENSP00000478222.3",
"transcript_support_level": 5,
"aa_start": 1172,
"aa_end": null,
"aa_length": 1605,
"cds_start": 3514,
"cds_end": null,
"cds_length": 4818,
"cdna_start": 4136,
"cdna_end": null,
"cdna_length": 6742,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "c.3361G>A",
"hgvs_p": "p.Gly1121Arg",
"transcript": "ENST00000714330.1",
"protein_id": "ENSP00000519606.1",
"transcript_support_level": null,
"aa_start": 1121,
"aa_end": null,
"aa_length": 1554,
"cds_start": 3361,
"cds_end": null,
"cds_length": 4665,
"cdna_start": 3536,
"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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "n.*1302G>A",
"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
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "n.*1302G>A",
"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": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "n.*1302G>A",
"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
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "n.*1302G>A",
"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
}
],
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"dbsnp": "rs113994112",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9814106225967407,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.962,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9863,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.58,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.282,
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Strong,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000375820.10",
"gene_symbol": "COL4A1",
"hgnc_id": 2202,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.3706G>A",
"hgvs_p": "p.Gly1236Arg"
}
],
"clinvar_disease": "Brain small vessel disease 1 with or without ocular anomalies,not provided",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1 O:1",
"phenotype_combined": "Brain small vessel disease 1 with or without ocular anomalies|not provided",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}