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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: 6-33164453-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=33164453&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 33164453,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000341947.7",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 65,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.4884G>C",
"hgvs_p": "p.Glu1628Asp",
"transcript": "NM_080680.3",
"protein_id": "NP_542411.2",
"transcript_support_level": null,
"aa_start": 1628,
"aa_end": null,
"aa_length": 1736,
"cds_start": 4884,
"cds_end": null,
"cds_length": 5211,
"cdna_start": 5111,
"cdna_end": null,
"cdna_length": 6422,
"mane_select": "ENST00000341947.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 65,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.4884G>C",
"hgvs_p": "p.Glu1628Asp",
"transcript": "ENST00000341947.7",
"protein_id": "ENSP00000339915.2",
"transcript_support_level": 5,
"aa_start": 1628,
"aa_end": null,
"aa_length": 1736,
"cds_start": 4884,
"cds_end": null,
"cds_length": 5211,
"cdna_start": 5111,
"cdna_end": null,
"cdna_length": 6422,
"mane_select": "NM_080680.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 64,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.4704G>C",
"hgvs_p": "p.Glu1568Asp",
"transcript": "NM_001424108.1",
"protein_id": "NP_001411037.1",
"transcript_support_level": null,
"aa_start": 1568,
"aa_end": null,
"aa_length": 1676,
"cds_start": 4704,
"cds_end": null,
"cds_length": 5031,
"cdna_start": 4931,
"cdna_end": null,
"cdna_length": 6242,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 63,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.4626G>C",
"hgvs_p": "p.Glu1542Asp",
"transcript": "NM_080681.3",
"protein_id": "NP_542412.2",
"transcript_support_level": null,
"aa_start": 1542,
"aa_end": null,
"aa_length": 1650,
"cds_start": 4626,
"cds_end": null,
"cds_length": 4953,
"cdna_start": 4853,
"cdna_end": null,
"cdna_length": 6164,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 63,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.4626G>C",
"hgvs_p": "p.Glu1542Asp",
"transcript": "ENST00000374708.8",
"protein_id": "ENSP00000363840.4",
"transcript_support_level": 5,
"aa_start": 1542,
"aa_end": null,
"aa_length": 1650,
"cds_start": 4626,
"cds_end": null,
"cds_length": 4953,
"cdna_start": 4885,
"cdna_end": null,
"cdna_length": 6209,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 62,
"exon_rank_end": null,
"exon_count": 63,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.4563G>C",
"hgvs_p": "p.Glu1521Asp",
"transcript": "NM_080679.3",
"protein_id": "NP_542410.2",
"transcript_support_level": null,
"aa_start": 1521,
"aa_end": null,
"aa_length": 1629,
"cds_start": 4563,
"cds_end": null,
"cds_length": 4890,
"cdna_start": 4790,
"cdna_end": null,
"cdna_length": 6101,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 65,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.4038G>C",
"hgvs_p": "p.Glu1346Asp",
"transcript": "NM_001424109.1",
"protein_id": "NP_001411038.1",
"transcript_support_level": null,
"aa_start": 1346,
"aa_end": null,
"aa_length": 1454,
"cds_start": 4038,
"cds_end": null,
"cds_length": 4365,
"cdna_start": 4902,
"cdna_end": null,
"cdna_length": 6213,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 64,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.3858G>C",
"hgvs_p": "p.Glu1286Asp",
"transcript": "NM_001424110.1",
"protein_id": "NP_001411039.1",
"transcript_support_level": null,
"aa_start": 1286,
"aa_end": null,
"aa_length": 1394,
"cds_start": 3858,
"cds_end": null,
"cds_length": 4185,
"cdna_start": 4722,
"cdna_end": null,
"cdna_length": 6033,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 64,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.3858G>C",
"hgvs_p": "p.Glu1286Asp",
"transcript": "NM_001424111.1",
"protein_id": "NP_001411040.1",
"transcript_support_level": null,
"aa_start": 1286,
"aa_end": null,
"aa_length": 1394,
"cds_start": 3858,
"cds_end": null,
"cds_length": 4185,
"cdna_start": 4735,
"cdna_end": null,
"cdna_length": 6046,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.2838G>C",
"hgvs_p": "p.Glu946Asp",
"transcript": "NM_001424112.1",
"protein_id": "NP_001411041.1",
"transcript_support_level": null,
"aa_start": 946,
"aa_end": null,
"aa_length": 1054,
"cds_start": 2838,
"cds_end": null,
"cds_length": 3165,
"cdna_start": 3094,
"cdna_end": null,
"cdna_length": 4405,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 66,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.4884G>C",
"hgvs_p": "p.Glu1628Asp",
"transcript": "XM_017010250.2",
"protein_id": "XP_016865739.1",
"transcript_support_level": null,
"aa_start": 1628,
"aa_end": null,
"aa_length": 1736,
"cds_start": 4884,
"cds_end": null,
"cds_length": 5211,
"cdna_start": 5376,
"cdna_end": null,
"cdna_length": 6687,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 60,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.4170G>C",
"hgvs_p": "p.Glu1390Asp",
"transcript": "XM_011514299.3",
"protein_id": "XP_011512601.1",
"transcript_support_level": null,
"aa_start": 1390,
"aa_end": null,
"aa_length": 1498,
"cds_start": 4170,
"cds_end": null,
"cds_length": 4497,
"cdna_start": 4469,
"cdna_end": null,
"cdna_length": 5780,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 65,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.4038G>C",
"hgvs_p": "p.Glu1346Asp",
"transcript": "XM_047418183.1",
"protein_id": "XP_047274139.1",
"transcript_support_level": null,
"aa_start": 1346,
"aa_end": null,
"aa_length": 1454,
"cds_start": 4038,
"cds_end": null,
"cds_length": 4365,
"cdna_start": 4915,
"cdna_end": null,
"cdna_length": 6226,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 59,
"exon_rank_end": null,
"exon_count": 60,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.3990G>C",
"hgvs_p": "p.Glu1330Asp",
"transcript": "XM_011514300.3",
"protein_id": "XP_011512602.1",
"transcript_support_level": null,
"aa_start": 1330,
"aa_end": null,
"aa_length": 1438,
"cds_start": 3990,
"cds_end": null,
"cds_length": 4317,
"cdna_start": 4289,
"cdna_end": null,
"cdna_length": 5600,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 58,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.3771G>C",
"hgvs_p": "p.Glu1257Asp",
"transcript": "XM_011514302.3",
"protein_id": "XP_011512604.1",
"transcript_support_level": null,
"aa_start": 1257,
"aa_end": null,
"aa_length": 1365,
"cds_start": 3771,
"cds_end": null,
"cds_length": 4098,
"cdna_start": 4426,
"cdna_end": null,
"cdna_length": 5737,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 58,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.3702G>C",
"hgvs_p": "p.Glu1234Asp",
"transcript": "XM_017010251.3",
"protein_id": "XP_016865740.1",
"transcript_support_level": null,
"aa_start": 1234,
"aa_end": null,
"aa_length": 1342,
"cds_start": 3702,
"cds_end": null,
"cds_length": 4029,
"cdna_start": 4245,
"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": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "n.674G>C",
"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": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "n.690G>C",
"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": "rs2229790",
"frequency_reference_population": 0.0007719958,
"hom_count_reference_population": 137,
"allele_count_reference_population": 1210,
"gnomad_exomes_af": 0.000775128,
"gnomad_genomes_af": 0.000742854,
"gnomad_exomes_ac": 1097,
"gnomad_genomes_ac": 113,
"gnomad_exomes_homalt": 125,
"gnomad_genomes_homalt": 12,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0053469836711883545,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.05,
"revel_prediction": "Benign",
"alphamissense_score": 0.0928,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.225,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000341947.7",
"gene_symbol": "COL11A2",
"hgnc_id": 2187,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.4884G>C",
"hgvs_p": "p.Glu1628Asp"
}
],
"clinvar_disease": " Dominant, autosomal dominant, autosomal recessive,COL11A2-related disorder,Connective tissue disorder,Fibrochondrogenesis 2,Otospondylomegaepiphyseal dysplasia,Stickler Syndrome,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:6 B:6",
"phenotype_combined": "not specified|Fibrochondrogenesis 2|Otospondylomegaepiphyseal dysplasia, autosomal recessive|Stickler Syndrome, Dominant|Otospondylomegaepiphyseal dysplasia, autosomal dominant|not provided|Connective tissue disorder|COL11A2-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}