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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: 6-33165647-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=33165647&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 33165647,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000341947.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 63,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.4652G>A",
"hgvs_p": "p.Arg1551Gln",
"transcript": "NM_080680.3",
"protein_id": "NP_542411.2",
"transcript_support_level": null,
"aa_start": 1551,
"aa_end": null,
"aa_length": 1736,
"cds_start": 4652,
"cds_end": null,
"cds_length": 5211,
"cdna_start": 4879,
"cdna_end": null,
"cdna_length": 6422,
"mane_select": "ENST00000341947.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 63,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.4652G>A",
"hgvs_p": "p.Arg1551Gln",
"transcript": "ENST00000341947.7",
"protein_id": "ENSP00000339915.2",
"transcript_support_level": 5,
"aa_start": 1551,
"aa_end": null,
"aa_length": 1736,
"cds_start": 4652,
"cds_end": null,
"cds_length": 5211,
"cdna_start": 4879,
"cdna_end": null,
"cdna_length": 6422,
"mane_select": "NM_080680.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 62,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.4472G>A",
"hgvs_p": "p.Arg1491Gln",
"transcript": "NM_001424108.1",
"protein_id": "NP_001411037.1",
"transcript_support_level": null,
"aa_start": 1491,
"aa_end": null,
"aa_length": 1676,
"cds_start": 4472,
"cds_end": null,
"cds_length": 5031,
"cdna_start": 4699,
"cdna_end": null,
"cdna_length": 6242,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 61,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.4394G>A",
"hgvs_p": "p.Arg1465Gln",
"transcript": "NM_080681.3",
"protein_id": "NP_542412.2",
"transcript_support_level": null,
"aa_start": 1465,
"aa_end": null,
"aa_length": 1650,
"cds_start": 4394,
"cds_end": null,
"cds_length": 4953,
"cdna_start": 4621,
"cdna_end": null,
"cdna_length": 6164,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 61,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.4394G>A",
"hgvs_p": "p.Arg1465Gln",
"transcript": "ENST00000374708.8",
"protein_id": "ENSP00000363840.4",
"transcript_support_level": 5,
"aa_start": 1465,
"aa_end": null,
"aa_length": 1650,
"cds_start": 4394,
"cds_end": null,
"cds_length": 4953,
"cdna_start": 4653,
"cdna_end": null,
"cdna_length": 6209,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 60,
"exon_rank_end": null,
"exon_count": 63,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.4331G>A",
"hgvs_p": "p.Arg1444Gln",
"transcript": "NM_080679.3",
"protein_id": "NP_542410.2",
"transcript_support_level": null,
"aa_start": 1444,
"aa_end": null,
"aa_length": 1629,
"cds_start": 4331,
"cds_end": null,
"cds_length": 4890,
"cdna_start": 4558,
"cdna_end": null,
"cdna_length": 6101,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 63,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.3806G>A",
"hgvs_p": "p.Arg1269Gln",
"transcript": "NM_001424109.1",
"protein_id": "NP_001411038.1",
"transcript_support_level": null,
"aa_start": 1269,
"aa_end": null,
"aa_length": 1454,
"cds_start": 3806,
"cds_end": null,
"cds_length": 4365,
"cdna_start": 4670,
"cdna_end": null,
"cdna_length": 6213,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 62,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.3626G>A",
"hgvs_p": "p.Arg1209Gln",
"transcript": "NM_001424110.1",
"protein_id": "NP_001411039.1",
"transcript_support_level": null,
"aa_start": 1209,
"aa_end": null,
"aa_length": 1394,
"cds_start": 3626,
"cds_end": null,
"cds_length": 4185,
"cdna_start": 4490,
"cdna_end": null,
"cdna_length": 6033,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 62,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.3626G>A",
"hgvs_p": "p.Arg1209Gln",
"transcript": "NM_001424111.1",
"protein_id": "NP_001411040.1",
"transcript_support_level": null,
"aa_start": 1209,
"aa_end": null,
"aa_length": 1394,
"cds_start": 3626,
"cds_end": null,
"cds_length": 4185,
"cdna_start": 4503,
"cdna_end": null,
"cdna_length": 6046,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.2606G>A",
"hgvs_p": "p.Arg869Gln",
"transcript": "NM_001424112.1",
"protein_id": "NP_001411041.1",
"transcript_support_level": null,
"aa_start": 869,
"aa_end": null,
"aa_length": 1054,
"cds_start": 2606,
"cds_end": null,
"cds_length": 3165,
"cdna_start": 2862,
"cdna_end": null,
"cdna_length": 4405,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 64,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.4652G>A",
"hgvs_p": "p.Arg1551Gln",
"transcript": "XM_017010250.2",
"protein_id": "XP_016865739.1",
"transcript_support_level": null,
"aa_start": 1551,
"aa_end": null,
"aa_length": 1736,
"cds_start": 4652,
"cds_end": null,
"cds_length": 5211,
"cdna_start": 5144,
"cdna_end": null,
"cdna_length": 6687,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 58,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.3938G>A",
"hgvs_p": "p.Arg1313Gln",
"transcript": "XM_011514299.3",
"protein_id": "XP_011512601.1",
"transcript_support_level": null,
"aa_start": 1313,
"aa_end": null,
"aa_length": 1498,
"cds_start": 3938,
"cds_end": null,
"cds_length": 4497,
"cdna_start": 4237,
"cdna_end": null,
"cdna_length": 5780,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 63,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.3806G>A",
"hgvs_p": "p.Arg1269Gln",
"transcript": "XM_047418183.1",
"protein_id": "XP_047274139.1",
"transcript_support_level": null,
"aa_start": 1269,
"aa_end": null,
"aa_length": 1454,
"cds_start": 3806,
"cds_end": null,
"cds_length": 4365,
"cdna_start": 4683,
"cdna_end": null,
"cdna_length": 6226,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 57,
"exon_rank_end": null,
"exon_count": 60,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.3758G>A",
"hgvs_p": "p.Arg1253Gln",
"transcript": "XM_011514300.3",
"protein_id": "XP_011512602.1",
"transcript_support_level": null,
"aa_start": 1253,
"aa_end": null,
"aa_length": 1438,
"cds_start": 3758,
"cds_end": null,
"cds_length": 4317,
"cdna_start": 4057,
"cdna_end": null,
"cdna_length": 5600,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 56,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.3539G>A",
"hgvs_p": "p.Arg1180Gln",
"transcript": "XM_011514302.3",
"protein_id": "XP_011512604.1",
"transcript_support_level": null,
"aa_start": 1180,
"aa_end": null,
"aa_length": 1365,
"cds_start": 3539,
"cds_end": null,
"cds_length": 4098,
"cdna_start": 4194,
"cdna_end": null,
"cdna_length": 5737,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 56,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.3470G>A",
"hgvs_p": "p.Arg1157Gln",
"transcript": "XM_017010251.3",
"protein_id": "XP_016865740.1",
"transcript_support_level": null,
"aa_start": 1157,
"aa_end": null,
"aa_length": 1342,
"cds_start": 3470,
"cds_end": null,
"cds_length": 4029,
"cdna_start": 4013,
"cdna_end": null,
"cdna_length": 5556,
"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": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "n.442G>A",
"hgvs_p": null,
"transcript": "ENST00000477772.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 1984,
"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": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "n.458G>A",
"hgvs_p": null,
"transcript": "ENST00000683572.1",
"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": 1313,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"dbsnp": "rs145343609",
"frequency_reference_population": 0.001090146,
"hom_count_reference_population": 3,
"allele_count_reference_population": 1758,
"gnomad_exomes_af": 0.00112775,
"gnomad_genomes_af": 0.000729294,
"gnomad_exomes_ac": 1647,
"gnomad_genomes_ac": 111,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.11764419078826904,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.25999999046325684,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.45,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1197,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.12,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.926,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.26,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000341947.7",
"gene_symbol": "COL11A2",
"hgnc_id": 2187,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.4652G>A",
"hgvs_p": "p.Arg1551Gln"
}
],
"clinvar_disease": " Dominant, autosomal dominant, autosomal recessive,COL11A2-related disorder,Fibrochondrogenesis 2,Otospondylomegaepiphyseal dysplasia,Stickler Syndrome,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:5 LB:5 O:1",
"phenotype_combined": "not specified|Stickler Syndrome, Dominant|Otospondylomegaepiphyseal dysplasia, autosomal recessive|Otospondylomegaepiphyseal dysplasia, autosomal dominant|Fibrochondrogenesis 2|not provided|COL11A2-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}