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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: 13-110469273-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=110469273&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 110469273,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000360467.7",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A2",
"gene_hgnc_id": 2203,
"hgvs_c": "c.2152C>T",
"hgvs_p": "p.Pro718Ser",
"transcript": "NM_001846.4",
"protein_id": "NP_001837.2",
"transcript_support_level": null,
"aa_start": 718,
"aa_end": null,
"aa_length": 1712,
"cds_start": 2152,
"cds_end": null,
"cds_length": 5139,
"cdna_start": 2441,
"cdna_end": null,
"cdna_length": 6446,
"mane_select": "ENST00000360467.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A2",
"gene_hgnc_id": 2203,
"hgvs_c": "c.2152C>T",
"hgvs_p": "p.Pro718Ser",
"transcript": "ENST00000360467.7",
"protein_id": "ENSP00000353654.5",
"transcript_support_level": 5,
"aa_start": 718,
"aa_end": null,
"aa_length": 1712,
"cds_start": 2152,
"cds_end": null,
"cds_length": 5139,
"cdna_start": 2441,
"cdna_end": null,
"cdna_length": 6446,
"mane_select": "NM_001846.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A2",
"gene_hgnc_id": 2203,
"hgvs_c": "c.2233C>T",
"hgvs_p": "p.Pro745Ser",
"transcript": "ENST00000714399.1",
"protein_id": "ENSP00000519666.1",
"transcript_support_level": null,
"aa_start": 745,
"aa_end": null,
"aa_length": 1739,
"cds_start": 2233,
"cds_end": null,
"cds_length": 5220,
"cdna_start": 2522,
"cdna_end": null,
"cdna_length": 6345,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A2",
"gene_hgnc_id": 2203,
"hgvs_c": "c.2152C>T",
"hgvs_p": "p.Pro718Ser",
"transcript": "ENST00000400163.8",
"protein_id": "ENSP00000383027.4",
"transcript_support_level": 5,
"aa_start": 718,
"aa_end": null,
"aa_length": 1712,
"cds_start": 2152,
"cds_end": null,
"cds_length": 5139,
"cdna_start": 2328,
"cdna_end": null,
"cdna_length": 6333,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A2",
"gene_hgnc_id": 2203,
"hgvs_c": "c.2152C>T",
"hgvs_p": "p.Pro718Ser",
"transcript": "ENST00000480609.2",
"protein_id": "ENSP00000497080.2",
"transcript_support_level": 2,
"aa_start": 718,
"aa_end": null,
"aa_length": 1651,
"cds_start": 2152,
"cds_end": null,
"cds_length": 4956,
"cdna_start": 2441,
"cdna_end": null,
"cdna_length": 5279,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A2",
"gene_hgnc_id": 2203,
"hgvs_c": "c.2152C>T",
"hgvs_p": "p.Pro718Ser",
"transcript": "ENST00000714396.1",
"protein_id": "ENSP00000519663.1",
"transcript_support_level": null,
"aa_start": 718,
"aa_end": null,
"aa_length": 1638,
"cds_start": 2152,
"cds_end": null,
"cds_length": 4917,
"cdna_start": 2449,
"cdna_end": null,
"cdna_length": 6050,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A2",
"gene_hgnc_id": 2203,
"hgvs_c": "c.2152C>T",
"hgvs_p": "p.Pro718Ser",
"transcript": "ENST00000649951.2",
"protein_id": "ENSP00000497015.2",
"transcript_support_level": null,
"aa_start": 718,
"aa_end": null,
"aa_length": 1469,
"cds_start": 2152,
"cds_end": null,
"cds_length": 4410,
"cdna_start": 2441,
"cdna_end": null,
"cdna_length": 5022,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A2",
"gene_hgnc_id": 2203,
"hgvs_c": "c.2152C>T",
"hgvs_p": "p.Pro718Ser",
"transcript": "ENST00000494852.3",
"protein_id": "ENSP00000497664.2",
"transcript_support_level": 3,
"aa_start": 718,
"aa_end": null,
"aa_length": 814,
"cds_start": 2152,
"cds_end": null,
"cds_length": 2445,
"cdna_start": 2450,
"cdna_end": null,
"cdna_length": 2851,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A2",
"gene_hgnc_id": 2203,
"hgvs_c": "n.2152C>T",
"hgvs_p": null,
"transcript": "ENST00000714397.1",
"protein_id": "ENSP00000519664.1",
"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": 6363,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A2",
"gene_hgnc_id": 2203,
"hgvs_c": "n.2152C>T",
"hgvs_p": null,
"transcript": "ENST00000714398.1",
"protein_id": "ENSP00000519665.1",
"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": 6547,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL4A2",
"gene_hgnc_id": 2203,
"dbsnp": "rs9583500",
"frequency_reference_population": 0.19924992,
"hom_count_reference_population": 34521,
"allele_count_reference_population": 319247,
"gnomad_exomes_af": 0.196419,
"gnomad_genomes_af": 0.226243,
"gnomad_exomes_ac": 284844,
"gnomad_genomes_ac": 34403,
"gnomad_exomes_homalt": 30136,
"gnomad_genomes_homalt": 4385,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0032528042793273926,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.299,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0828,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.31,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.924,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000360467.7",
"gene_symbol": "COL4A2",
"hgnc_id": 2203,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2152C>T",
"hgvs_p": "p.Pro718Ser"
}
],
"clinvar_disease": "Porencephaly 2,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"phenotype_combined": "Porencephaly 2|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}