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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: 6-33185042-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=33185042&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 33185042,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000341947.7",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.889G>A",
"hgvs_p": "p.Gly297Ser",
"transcript": "NM_080680.3",
"protein_id": "NP_542411.2",
"transcript_support_level": null,
"aa_start": 297,
"aa_end": null,
"aa_length": 1736,
"cds_start": 889,
"cds_end": null,
"cds_length": 5211,
"cdna_start": 1116,
"cdna_end": null,
"cdna_length": 6422,
"mane_select": "ENST00000341947.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.889G>A",
"hgvs_p": "p.Gly297Ser",
"transcript": "ENST00000341947.7",
"protein_id": "ENSP00000339915.2",
"transcript_support_level": 5,
"aa_start": 297,
"aa_end": null,
"aa_length": 1736,
"cds_start": 889,
"cds_end": null,
"cds_length": 5211,
"cdna_start": 1116,
"cdna_end": null,
"cdna_length": 6422,
"mane_select": "NM_080680.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.889G>A",
"hgvs_p": "p.Gly297Ser",
"transcript": "NM_001424108.1",
"protein_id": "NP_001411037.1",
"transcript_support_level": null,
"aa_start": 297,
"aa_end": null,
"aa_length": 1676,
"cds_start": 889,
"cds_end": null,
"cds_length": 5031,
"cdna_start": 1116,
"cdna_end": null,
"cdna_length": 6242,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.811G>A",
"hgvs_p": "p.Gly271Ser",
"transcript": "NM_080681.3",
"protein_id": "NP_542412.2",
"transcript_support_level": null,
"aa_start": 271,
"aa_end": null,
"aa_length": 1650,
"cds_start": 811,
"cds_end": null,
"cds_length": 4953,
"cdna_start": 1038,
"cdna_end": null,
"cdna_length": 6164,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.811G>A",
"hgvs_p": "p.Gly271Ser",
"transcript": "ENST00000374708.8",
"protein_id": "ENSP00000363840.4",
"transcript_support_level": 5,
"aa_start": 271,
"aa_end": null,
"aa_length": 1650,
"cds_start": 811,
"cds_end": null,
"cds_length": 4953,
"cdna_start": 1070,
"cdna_end": null,
"cdna_length": 6209,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.43G>A",
"hgvs_p": "p.Gly15Ser",
"transcript": "NM_001424109.1",
"protein_id": "NP_001411038.1",
"transcript_support_level": null,
"aa_start": 15,
"aa_end": null,
"aa_length": 1454,
"cds_start": 43,
"cds_end": null,
"cds_length": 4365,
"cdna_start": 907,
"cdna_end": null,
"cdna_length": 6213,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.43G>A",
"hgvs_p": "p.Gly15Ser",
"transcript": "NM_001424110.1",
"protein_id": "NP_001411039.1",
"transcript_support_level": null,
"aa_start": 15,
"aa_end": null,
"aa_length": 1394,
"cds_start": 43,
"cds_end": null,
"cds_length": 4185,
"cdna_start": 907,
"cdna_end": null,
"cdna_length": 6033,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.43G>A",
"hgvs_p": "p.Gly15Ser",
"transcript": "NM_001424111.1",
"protein_id": "NP_001411040.1",
"transcript_support_level": null,
"aa_start": 15,
"aa_end": null,
"aa_length": 1394,
"cds_start": 43,
"cds_end": null,
"cds_length": 4185,
"cdna_start": 920,
"cdna_end": null,
"cdna_length": 6046,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.889G>A",
"hgvs_p": "p.Gly297Ser",
"transcript": "XM_017010250.2",
"protein_id": "XP_016865739.1",
"transcript_support_level": null,
"aa_start": 297,
"aa_end": null,
"aa_length": 1736,
"cds_start": 889,
"cds_end": null,
"cds_length": 5211,
"cdna_start": 1381,
"cdna_end": null,
"cdna_length": 6687,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.175G>A",
"hgvs_p": "p.Gly59Ser",
"transcript": "XM_011514299.3",
"protein_id": "XP_011512601.1",
"transcript_support_level": null,
"aa_start": 59,
"aa_end": null,
"aa_length": 1498,
"cds_start": 175,
"cds_end": null,
"cds_length": 4497,
"cdna_start": 474,
"cdna_end": null,
"cdna_length": 5780,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.43G>A",
"hgvs_p": "p.Gly15Ser",
"transcript": "XM_047418183.1",
"protein_id": "XP_047274139.1",
"transcript_support_level": null,
"aa_start": 15,
"aa_end": null,
"aa_length": 1454,
"cds_start": 43,
"cds_end": null,
"cds_length": 4365,
"cdna_start": 920,
"cdna_end": null,
"cdna_length": 6226,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 60,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.175G>A",
"hgvs_p": "p.Gly59Ser",
"transcript": "XM_011514300.3",
"protein_id": "XP_011512602.1",
"transcript_support_level": null,
"aa_start": 59,
"aa_end": null,
"aa_length": 1438,
"cds_start": 175,
"cds_end": null,
"cds_length": 4317,
"cdna_start": 474,
"cdna_end": null,
"cdna_length": 5600,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "n.706G>A",
"hgvs_p": null,
"transcript": "ENST00000682718.1",
"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": 1380,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 63,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.798+1585G>A",
"hgvs_p": null,
"transcript": "NM_080679.3",
"protein_id": "NP_542410.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1629,
"cds_start": -4,
"cds_end": null,
"cds_length": 4890,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6101,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"dbsnp": "rs139116571",
"frequency_reference_population": 0.000121196805,
"hom_count_reference_population": 0,
"allele_count_reference_population": 188,
"gnomad_exomes_af": 0.000122225,
"gnomad_genomes_af": 0.000111738,
"gnomad_exomes_ac": 171,
"gnomad_genomes_ac": 17,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.12054944038391113,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.181,
"revel_prediction": "Benign",
"alphamissense_score": 0.0698,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.23,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.348,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000341947.7",
"gene_symbol": "COL11A2",
"hgnc_id": 2187,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.889G>A",
"hgvs_p": "p.Gly297Ser"
}
],
"clinvar_disease": " autosomal dominant, autosomal recessive,Autosomal dominant nonsyndromic hearing loss 13,Autosomal recessive nonsyndromic hearing loss 53,COL11A2-related disorder,Connective tissue disorder,Fibrochondrogenesis 2,Nonsyndromic genetic hearing loss,Otospondylomegaepiphyseal dysplasia,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:8 LB:1",
"phenotype_combined": "not specified|Autosomal dominant nonsyndromic hearing loss 13;Otospondylomegaepiphyseal dysplasia, autosomal dominant;Fibrochondrogenesis 2;Autosomal recessive nonsyndromic hearing loss 53;Otospondylomegaepiphyseal dysplasia, autosomal recessive|Autosomal dominant nonsyndromic hearing loss 13|Otospondylomegaepiphyseal dysplasia, autosomal dominant|not provided|Connective tissue disorder|COL11A2-related disorder|Nonsyndromic genetic hearing loss",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}