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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: 2-189043249-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=189043249&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "COL5A2",
"hgnc_id": 2210,
"hgvs_c": "c.3373G>C",
"hgvs_p": "p.Gly1125Arg",
"inheritance_mode": "AD",
"pathogenic_score": 6,
"score": 6,
"transcript": "NM_000393.5",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_score": 6,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.998,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.6,
"chr": "2",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": " 1, classic type,Ehlers-Danlos syndrome",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9869297742843628,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 1499,
"aa_ref": "G",
"aa_start": 1125,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6829,
"cdna_start": 3530,
"cds_end": null,
"cds_length": 4500,
"cds_start": 3373,
"consequences": [
"missense_variant"
],
"exon_count": 54,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "NM_000393.5",
"gene_hgnc_id": 2210,
"gene_symbol": "COL5A2",
"hgvs_c": "c.3373G>C",
"hgvs_p": "p.Gly1125Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000374866.9",
"protein_coding": true,
"protein_id": "NP_000384.2",
"strand": false,
"transcript": "NM_000393.5",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 1499,
"aa_ref": "G",
"aa_start": 1125,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6829,
"cdna_start": 3530,
"cds_end": null,
"cds_length": 4500,
"cds_start": 3373,
"consequences": [
"missense_variant"
],
"exon_count": 54,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "ENST00000374866.9",
"gene_hgnc_id": 2210,
"gene_symbol": "COL5A2",
"hgvs_c": "c.3373G>C",
"hgvs_p": "p.Gly1125Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000393.5",
"protein_coding": true,
"protein_id": "ENSP00000364000.3",
"strand": false,
"transcript": "ENST00000374866.9",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 1498,
"aa_ref": "G",
"aa_start": 1124,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5244,
"cdna_start": 3527,
"cds_end": null,
"cds_length": 4497,
"cds_start": 3370,
"consequences": [
"missense_variant"
],
"exon_count": 54,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "ENST00000858728.1",
"gene_hgnc_id": 2210,
"gene_symbol": "COL5A2",
"hgvs_c": "c.3370G>C",
"hgvs_p": "p.Gly1124Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000528787.1",
"strand": false,
"transcript": "ENST00000858728.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 1463,
"aa_ref": "G",
"aa_start": 1089,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4861,
"cdna_start": 3422,
"cds_end": null,
"cds_length": 4392,
"cds_start": 3265,
"consequences": [
"missense_variant"
],
"exon_count": 53,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000858729.1",
"gene_hgnc_id": 2210,
"gene_symbol": "COL5A2",
"hgvs_c": "c.3265G>C",
"hgvs_p": "p.Gly1089Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000528788.1",
"strand": false,
"transcript": "ENST00000858729.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 1112,
"aa_ref": "G",
"aa_start": 738,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6399,
"cdna_start": 3117,
"cds_end": null,
"cds_length": 3339,
"cds_start": 2212,
"consequences": [
"missense_variant"
],
"exon_count": 47,
"exon_rank": 41,
"exon_rank_end": null,
"feature": "ENST00000618828.1",
"gene_hgnc_id": 2210,
"gene_symbol": "COL5A2",
"hgvs_c": "c.2212G>C",
"hgvs_p": "p.Gly738Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000482184.1",
"strand": false,
"transcript": "ENST00000618828.1",
"transcript_support_level": 5
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 1453,
"aa_ref": "G",
"aa_start": 1079,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7124,
"cdna_start": 3825,
"cds_end": null,
"cds_length": 4362,
"cds_start": 3235,
"consequences": [
"missense_variant"
],
"exon_count": 57,
"exon_rank": 51,
"exon_rank_end": null,
"feature": "XM_011510573.4",
"gene_hgnc_id": 2210,
"gene_symbol": "COL5A2",
"hgvs_c": "c.3235G>C",
"hgvs_p": "p.Gly1079Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011508875.1",
"strand": false,
"transcript": "XM_011510573.4",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 1453,
"aa_ref": "G",
"aa_start": 1079,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7296,
"cdna_start": 3997,
"cds_end": null,
"cds_length": 4362,
"cds_start": 3235,
"consequences": [
"missense_variant"
],
"exon_count": 59,
"exon_rank": 53,
"exon_rank_end": null,
"feature": "XM_047443251.1",
"gene_hgnc_id": 2210,
"gene_symbol": "COL5A2",
"hgvs_c": "c.3235G>C",
"hgvs_p": "p.Gly1079Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047299207.1",
"strand": false,
"transcript": "XM_047443251.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 1453,
"aa_ref": "G",
"aa_start": 1079,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7078,
"cdna_start": 3779,
"cds_end": null,
"cds_length": 4362,
"cds_start": 3235,
"consequences": [
"missense_variant"
],
"exon_count": 58,
"exon_rank": 52,
"exon_rank_end": null,
"feature": "XM_047443252.1",
"gene_hgnc_id": 2210,
"gene_symbol": "COL5A2",
"hgvs_c": "c.3235G>C",
"hgvs_p": "p.Gly1079Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047299208.1",
"strand": false,
"transcript": "XM_047443252.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs151187317",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 2210,
"gene_symbol": "COL5A2",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Ehlers-Danlos syndrome, classic type, 1",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.882,
"pos": 189043249,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 1,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000393.5"
}
]
}