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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: 6-33178970-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=33178970&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 33178970,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000341947.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.1615C>T",
"hgvs_p": "p.Arg539Trp",
"transcript": "NM_080680.3",
"protein_id": "NP_542411.2",
"transcript_support_level": null,
"aa_start": 539,
"aa_end": null,
"aa_length": 1736,
"cds_start": 1615,
"cds_end": null,
"cds_length": 5211,
"cdna_start": 1842,
"cdna_end": null,
"cdna_length": 6422,
"mane_select": "ENST00000341947.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.1615C>T",
"hgvs_p": "p.Arg539Trp",
"transcript": "ENST00000341947.7",
"protein_id": "ENSP00000339915.2",
"transcript_support_level": 5,
"aa_start": 539,
"aa_end": null,
"aa_length": 1736,
"cds_start": 1615,
"cds_end": null,
"cds_length": 5211,
"cdna_start": 1842,
"cdna_end": null,
"cdna_length": 6422,
"mane_select": "NM_080680.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.1435C>T",
"hgvs_p": "p.Arg479Trp",
"transcript": "NM_001424108.1",
"protein_id": "NP_001411037.1",
"transcript_support_level": null,
"aa_start": 479,
"aa_end": null,
"aa_length": 1676,
"cds_start": 1435,
"cds_end": null,
"cds_length": 5031,
"cdna_start": 1662,
"cdna_end": null,
"cdna_length": 6242,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.1357C>T",
"hgvs_p": "p.Arg453Trp",
"transcript": "NM_080681.3",
"protein_id": "NP_542412.2",
"transcript_support_level": null,
"aa_start": 453,
"aa_end": null,
"aa_length": 1650,
"cds_start": 1357,
"cds_end": null,
"cds_length": 4953,
"cdna_start": 1584,
"cdna_end": null,
"cdna_length": 6164,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.1357C>T",
"hgvs_p": "p.Arg453Trp",
"transcript": "ENST00000374708.8",
"protein_id": "ENSP00000363840.4",
"transcript_support_level": 5,
"aa_start": 453,
"aa_end": null,
"aa_length": 1650,
"cds_start": 1357,
"cds_end": null,
"cds_length": 4953,
"cdna_start": 1616,
"cdna_end": null,
"cdna_length": 6209,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 63,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.1294C>T",
"hgvs_p": "p.Arg432Trp",
"transcript": "NM_080679.3",
"protein_id": "NP_542410.2",
"transcript_support_level": null,
"aa_start": 432,
"aa_end": null,
"aa_length": 1629,
"cds_start": 1294,
"cds_end": null,
"cds_length": 4890,
"cdna_start": 1521,
"cdna_end": null,
"cdna_length": 6101,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.769C>T",
"hgvs_p": "p.Arg257Trp",
"transcript": "NM_001424109.1",
"protein_id": "NP_001411038.1",
"transcript_support_level": null,
"aa_start": 257,
"aa_end": null,
"aa_length": 1454,
"cds_start": 769,
"cds_end": null,
"cds_length": 4365,
"cdna_start": 1633,
"cdna_end": null,
"cdna_length": 6213,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.589C>T",
"hgvs_p": "p.Arg197Trp",
"transcript": "NM_001424110.1",
"protein_id": "NP_001411039.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 1394,
"cds_start": 589,
"cds_end": null,
"cds_length": 4185,
"cdna_start": 1453,
"cdna_end": null,
"cdna_length": 6033,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.589C>T",
"hgvs_p": "p.Arg197Trp",
"transcript": "NM_001424111.1",
"protein_id": "NP_001411040.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 1394,
"cds_start": 589,
"cds_end": null,
"cds_length": 4185,
"cdna_start": 1466,
"cdna_end": null,
"cdna_length": 6046,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.241C>T",
"hgvs_p": "p.Arg81Trp",
"transcript": "ENST00000361917.6",
"protein_id": "ENSP00000355123.2",
"transcript_support_level": 5,
"aa_start": 81,
"aa_end": null,
"aa_length": 433,
"cds_start": 241,
"cds_end": null,
"cds_length": 1303,
"cdna_start": 242,
"cdna_end": null,
"cdna_length": 1304,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.1615C>T",
"hgvs_p": "p.Arg539Trp",
"transcript": "XM_017010250.2",
"protein_id": "XP_016865739.1",
"transcript_support_level": null,
"aa_start": 539,
"aa_end": null,
"aa_length": 1736,
"cds_start": 1615,
"cds_end": null,
"cds_length": 5211,
"cdna_start": 2107,
"cdna_end": null,
"cdna_length": 6687,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.901C>T",
"hgvs_p": "p.Arg301Trp",
"transcript": "XM_011514299.3",
"protein_id": "XP_011512601.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 1498,
"cds_start": 901,
"cds_end": null,
"cds_length": 4497,
"cdna_start": 1200,
"cdna_end": null,
"cdna_length": 5780,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.769C>T",
"hgvs_p": "p.Arg257Trp",
"transcript": "XM_047418183.1",
"protein_id": "XP_047274139.1",
"transcript_support_level": null,
"aa_start": 257,
"aa_end": null,
"aa_length": 1454,
"cds_start": 769,
"cds_end": null,
"cds_length": 4365,
"cdna_start": 1646,
"cdna_end": null,
"cdna_length": 6226,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 60,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.721C>T",
"hgvs_p": "p.Arg241Trp",
"transcript": "XM_011514300.3",
"protein_id": "XP_011512602.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 1438,
"cds_start": 721,
"cds_end": null,
"cds_length": 4317,
"cdna_start": 1020,
"cdna_end": null,
"cdna_length": 5600,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.502C>T",
"hgvs_p": "p.Arg168Trp",
"transcript": "XM_011514302.3",
"protein_id": "XP_011512604.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 1365,
"cds_start": 502,
"cds_end": null,
"cds_length": 4098,
"cdna_start": 1157,
"cdna_end": null,
"cdna_length": 5737,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.433C>T",
"hgvs_p": "p.Arg145Trp",
"transcript": "XM_017010251.3",
"protein_id": "XP_016865740.1",
"transcript_support_level": null,
"aa_start": 145,
"aa_end": null,
"aa_length": 1342,
"cds_start": 433,
"cds_end": null,
"cds_length": 4029,
"cdna_start": 976,
"cdna_end": null,
"cdna_length": 5556,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"dbsnp": "rs145499142",
"frequency_reference_population": 0.0024553111,
"hom_count_reference_population": 12,
"allele_count_reference_population": 3963,
"gnomad_exomes_af": 0.00254952,
"gnomad_genomes_af": 0.00155049,
"gnomad_exomes_ac": 3727,
"gnomad_genomes_ac": 236,
"gnomad_exomes_homalt": 11,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.17189928889274597,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.603,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5434,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.09,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.198,
"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": -11,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -11,
"benign_score": 11,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000341947.7",
"gene_symbol": "COL11A2",
"hgnc_id": 2187,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1615C>T",
"hgvs_p": "p.Arg539Trp"
}
],
"clinvar_disease": " Dominant, autosomal dominant, autosomal recessive,Connective tissue 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:4 LB:5 B:3 O:1",
"phenotype_combined": "not specified|Fibrochondrogenesis 2|Otospondylomegaepiphyseal dysplasia, autosomal recessive|Otospondylomegaepiphyseal dysplasia, autosomal dominant|Stickler Syndrome, Dominant|Connective tissue disorder|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}