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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: 20-62824471-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=62824471&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 19,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "COL9A3",
"hgnc_id": 2219,
"hgvs_c": "c.546C>T",
"hgvs_p": "p.Pro182Pro",
"inheritance_mode": "AR,AD",
"pathogenic_score": 0,
"score": -19,
"transcript": "NM_001853.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_score": -19,
"allele_count_reference_population": 18347,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.46,
"chr": "20",
"clinvar_classification": "Benign",
"clinvar_disease": "Connective tissue disorder,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:8",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.46000000834465027,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 684,
"aa_ref": "P",
"aa_start": 182,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2497,
"cdna_start": 561,
"cds_end": null,
"cds_length": 2055,
"cds_start": 546,
"consequences": [
"synonymous_variant"
],
"exon_count": 32,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_001853.4",
"gene_hgnc_id": 2219,
"gene_symbol": "COL9A3",
"hgvs_c": "c.546C>T",
"hgvs_p": "p.Pro182Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000649368.1",
"protein_coding": true,
"protein_id": "NP_001844.3",
"strand": true,
"transcript": "NM_001853.4",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 684,
"aa_ref": "P",
"aa_start": 182,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2497,
"cdna_start": 561,
"cds_end": null,
"cds_length": 2055,
"cds_start": 546,
"consequences": [
"synonymous_variant"
],
"exon_count": 32,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000649368.1",
"gene_hgnc_id": 2219,
"gene_symbol": "COL9A3",
"hgvs_c": "c.546C>T",
"hgvs_p": "p.Pro182Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001853.4",
"protein_coding": true,
"protein_id": "ENSP00000496793.1",
"strand": true,
"transcript": "ENST00000649368.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 701,
"aa_ref": "P",
"aa_start": 199,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2482,
"cdna_start": 612,
"cds_end": null,
"cds_length": 2106,
"cds_start": 597,
"consequences": [
"synonymous_variant"
],
"exon_count": 33,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000934236.1",
"gene_hgnc_id": 2219,
"gene_symbol": "COL9A3",
"hgvs_c": "c.597C>T",
"hgvs_p": "p.Pro199Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604295.1",
"strand": true,
"transcript": "ENST00000934236.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 660,
"aa_ref": "P",
"aa_start": 158,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2451,
"cdna_start": 511,
"cds_end": null,
"cds_length": 1983,
"cds_start": 474,
"consequences": [
"synonymous_variant"
],
"exon_count": 31,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000894732.1",
"gene_hgnc_id": 2219,
"gene_symbol": "COL9A3",
"hgvs_c": "c.474C>T",
"hgvs_p": "p.Pro158Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000564791.1",
"strand": true,
"transcript": "ENST00000894732.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 635,
"aa_ref": "P",
"aa_start": 182,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2391,
"cdna_start": 598,
"cds_end": null,
"cds_length": 1908,
"cds_start": 546,
"consequences": [
"synonymous_variant"
],
"exon_count": 31,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000934235.1",
"gene_hgnc_id": 2219,
"gene_symbol": "COL9A3",
"hgvs_c": "c.546C>T",
"hgvs_p": "p.Pro182Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604294.1",
"strand": true,
"transcript": "ENST00000934235.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 190,
"aa_ref": "P",
"aa_start": 145,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 617,
"cdna_start": 479,
"cds_end": null,
"cds_length": 573,
"cds_start": 435,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000452372.2",
"gene_hgnc_id": 2219,
"gene_symbol": "COL9A3",
"hgvs_c": "c.435C>T",
"hgvs_p": "p.Pro145Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000394280.1",
"strand": true,
"transcript": "ENST00000452372.2",
"transcript_support_level": 5
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 743,
"aa_ref": "P",
"aa_start": 241,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2921,
"cdna_start": 985,
"cds_end": null,
"cds_length": 2232,
"cds_start": 723,
"consequences": [
"synonymous_variant"
],
"exon_count": 31,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047439893.1",
"gene_hgnc_id": 2219,
"gene_symbol": "COL9A3",
"hgvs_c": "c.723C>T",
"hgvs_p": "p.Pro241Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047295849.1",
"strand": true,
"transcript": "XM_047439893.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 486,
"aa_ref": "P",
"aa_start": 182,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1554,
"cdna_start": 561,
"cds_end": null,
"cds_length": 1461,
"cds_start": 546,
"consequences": [
"synonymous_variant"
],
"exon_count": 28,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "XM_017027666.2",
"gene_hgnc_id": 2219,
"gene_symbol": "COL9A3",
"hgvs_c": "c.546C>T",
"hgvs_p": "p.Pro182Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016883155.1",
"strand": true,
"transcript": "XM_017027666.2",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 471,
"aa_ref": "P",
"aa_start": 182,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1589,
"cdna_start": 561,
"cds_end": null,
"cds_length": 1416,
"cds_start": 546,
"consequences": [
"synonymous_variant"
],
"exon_count": 28,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "XM_047439895.1",
"gene_hgnc_id": 2219,
"gene_symbol": "COL9A3",
"hgvs_c": "c.546C>T",
"hgvs_p": "p.Pro182Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047295851.1",
"strand": true,
"transcript": "XM_047439895.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 497,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2509,
"cdna_start": null,
"cds_end": null,
"cds_length": 1494,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 32,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "XM_047439894.1",
"gene_hgnc_id": 2219,
"gene_symbol": "COL9A3",
"hgvs_c": "c.-16C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047295850.1",
"strand": true,
"transcript": "XM_047439894.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 716,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000463487.2",
"gene_hgnc_id": 2219,
"gene_symbol": "COL9A3",
"hgvs_c": "n.51C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000463487.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 635,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000477612.5",
"gene_hgnc_id": 2219,
"gene_symbol": "COL9A3",
"hgvs_c": "n.542C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000477612.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 838,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000489045.5",
"gene_hgnc_id": 2219,
"gene_symbol": "COL9A3",
"hgvs_c": "n.592C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000489045.5",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs150148851",
"effect": "synonymous_variant",
"frequency_reference_population": 0.011469413,
"gene_hgnc_id": 2219,
"gene_symbol": "COL9A3",
"gnomad_exomes_ac": 17271,
"gnomad_exomes_af": 0.0119319,
"gnomad_exomes_homalt": 138,
"gnomad_genomes_ac": 1076,
"gnomad_genomes_af": 0.00707039,
"gnomad_genomes_homalt": 7,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 145,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not specified|not provided|Connective tissue disorder",
"phylop100way_prediction": "Benign",
"phylop100way_score": -5.76,
"pos": 62824471,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_001853.4"
}
]
}