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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: 13-110213999-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=110213999&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 110213999,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000375820.10",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "c.161C>T",
"hgvs_p": "p.Pro54Leu",
"transcript": "NM_001845.6",
"protein_id": "NP_001836.3",
"transcript_support_level": null,
"aa_start": 54,
"aa_end": null,
"aa_length": 1669,
"cds_start": 161,
"cds_end": null,
"cds_length": 5010,
"cdna_start": 291,
"cdna_end": null,
"cdna_length": 6540,
"mane_select": "ENST00000375820.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "c.161C>T",
"hgvs_p": "p.Pro54Leu",
"transcript": "ENST00000375820.10",
"protein_id": "ENSP00000364979.4",
"transcript_support_level": 1,
"aa_start": 54,
"aa_end": null,
"aa_length": 1669,
"cds_start": 161,
"cds_end": null,
"cds_length": 5010,
"cdna_start": 291,
"cdna_end": null,
"cdna_length": 6540,
"mane_select": "NM_001845.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "c.161C>T",
"hgvs_p": "p.Pro54Leu",
"transcript": "ENST00000543140.6",
"protein_id": "ENSP00000443348.1",
"transcript_support_level": 1,
"aa_start": 54,
"aa_end": null,
"aa_length": 519,
"cds_start": 161,
"cds_end": null,
"cds_length": 1560,
"cdna_start": 265,
"cdna_end": null,
"cdna_length": 2549,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "c.-32C>T",
"hgvs_p": null,
"transcript": "ENST00000615732.3",
"protein_id": "ENSP00000478222.3",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1605,
"cds_start": -4,
"cds_end": null,
"cds_length": 4818,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6742,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "c.161C>T",
"hgvs_p": "p.Pro54Leu",
"transcript": "ENST00000650424.2",
"protein_id": "ENSP00000497477.2",
"transcript_support_level": null,
"aa_start": 54,
"aa_end": null,
"aa_length": 1667,
"cds_start": 161,
"cds_end": null,
"cds_length": 5004,
"cdna_start": 291,
"cdna_end": null,
"cdna_length": 6386,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "c.161C>T",
"hgvs_p": "p.Pro54Leu",
"transcript": "ENST00000714330.1",
"protein_id": "ENSP00000519606.1",
"transcript_support_level": null,
"aa_start": 54,
"aa_end": null,
"aa_length": 1554,
"cds_start": 161,
"cds_end": null,
"cds_length": 4665,
"cdna_start": 336,
"cdna_end": null,
"cdna_length": 6240,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "c.161C>T",
"hgvs_p": "p.Pro54Leu",
"transcript": "NM_001303110.2",
"protein_id": "NP_001290039.1",
"transcript_support_level": null,
"aa_start": 54,
"aa_end": null,
"aa_length": 519,
"cds_start": 161,
"cds_end": null,
"cds_length": 1560,
"cdna_start": 291,
"cdna_end": null,
"cdna_length": 2575,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "c.161C>T",
"hgvs_p": "p.Pro54Leu",
"transcript": "ENST00000647797.2",
"protein_id": "ENSP00000497756.2",
"transcript_support_level": null,
"aa_start": 54,
"aa_end": null,
"aa_length": 454,
"cds_start": 161,
"cds_end": null,
"cds_length": 1365,
"cdna_start": 291,
"cdna_end": null,
"cdna_length": 2345,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "c.161C>T",
"hgvs_p": "p.Pro54Leu",
"transcript": "ENST00000648966.2",
"protein_id": "ENSP00000497533.2",
"transcript_support_level": null,
"aa_start": 54,
"aa_end": null,
"aa_length": 217,
"cds_start": 161,
"cds_end": null,
"cds_length": 654,
"cdna_start": 291,
"cdna_end": null,
"cdna_length": 836,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "c.161C>T",
"hgvs_p": "p.Pro54Leu",
"transcript": "ENST00000649484.2",
"protein_id": "ENSP00000497355.2",
"transcript_support_level": null,
"aa_start": 54,
"aa_end": null,
"aa_length": 188,
"cds_start": 161,
"cds_end": null,
"cds_length": 567,
"cdna_start": 291,
"cdna_end": null,
"cdna_length": 922,
"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": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "n.40C>T",
"hgvs_p": null,
"transcript": "ENST00000648170.1",
"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": 1372,
"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": 3,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "n.291C>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": 3,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "n.161C>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
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "n.161C>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": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"hgvs_c": "c.-32C>T",
"hgvs_p": null,
"transcript": "ENST00000615732.3",
"protein_id": "ENSP00000478222.3",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1605,
"cds_start": -4,
"cds_end": null,
"cds_length": 4818,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6742,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL4A1",
"gene_hgnc_id": 2202,
"dbsnp": "rs34004222",
"frequency_reference_population": 0.003947468,
"hom_count_reference_population": 22,
"allele_count_reference_population": 6371,
"gnomad_exomes_af": 0.00408388,
"gnomad_genomes_af": 0.00263642,
"gnomad_exomes_ac": 5970,
"gnomad_genomes_ac": 401,
"gnomad_exomes_homalt": 21,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01242375373840332,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.746,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1429,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.16,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.873,
"phylop100way_prediction": "Uncertain_significance",
"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": -11,
"acmg_classification": "Benign",
"acmg_criteria": "PM1,BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -11,
"benign_score": 13,
"pathogenic_score": 2,
"criteria": [
"PM1",
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000375820.10",
"gene_symbol": "COL4A1",
"hgnc_id": 2202,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.161C>T",
"hgvs_p": "p.Pro54Leu"
}
],
"clinvar_disease": "Autosomal dominant familial hematuria-retinal arteriolar tortuosity-contractures syndrome,Brain small vessel disease 1 with or without ocular anomalies,COL4A1-related disorder,Chronic kidney disease,Optic nerve hypoplasia,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:3 B:5",
"phenotype_combined": "not specified|Optic nerve hypoplasia|Autosomal dominant familial hematuria-retinal arteriolar tortuosity-contractures syndrome|not provided|Brain small vessel disease 1 with or without ocular anomalies|Chronic kidney disease|COL4A1-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}