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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: 6-33170061-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=33170061&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 33170061,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000341947.7",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.3622C>T",
"hgvs_p": "p.Pro1208Ser",
"transcript": "NM_080680.3",
"protein_id": "NP_542411.2",
"transcript_support_level": null,
"aa_start": 1208,
"aa_end": null,
"aa_length": 1736,
"cds_start": 3622,
"cds_end": null,
"cds_length": 5211,
"cdna_start": 3849,
"cdna_end": null,
"cdna_length": 6422,
"mane_select": "ENST00000341947.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.3622C>T",
"hgvs_p": "p.Pro1208Ser",
"transcript": "ENST00000341947.7",
"protein_id": "ENSP00000339915.2",
"transcript_support_level": 5,
"aa_start": 1208,
"aa_end": null,
"aa_length": 1736,
"cds_start": 3622,
"cds_end": null,
"cds_length": 5211,
"cdna_start": 3849,
"cdna_end": null,
"cdna_length": 6422,
"mane_select": "NM_080680.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 48,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.3442C>T",
"hgvs_p": "p.Pro1148Ser",
"transcript": "NM_001424108.1",
"protein_id": "NP_001411037.1",
"transcript_support_level": null,
"aa_start": 1148,
"aa_end": null,
"aa_length": 1676,
"cds_start": 3442,
"cds_end": null,
"cds_length": 5031,
"cdna_start": 3669,
"cdna_end": null,
"cdna_length": 6242,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.3364C>T",
"hgvs_p": "p.Pro1122Ser",
"transcript": "NM_080681.3",
"protein_id": "NP_542412.2",
"transcript_support_level": null,
"aa_start": 1122,
"aa_end": null,
"aa_length": 1650,
"cds_start": 3364,
"cds_end": null,
"cds_length": 4953,
"cdna_start": 3591,
"cdna_end": null,
"cdna_length": 6164,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.3364C>T",
"hgvs_p": "p.Pro1122Ser",
"transcript": "ENST00000374708.8",
"protein_id": "ENSP00000363840.4",
"transcript_support_level": 5,
"aa_start": 1122,
"aa_end": null,
"aa_length": 1650,
"cds_start": 3364,
"cds_end": null,
"cds_length": 4953,
"cdna_start": 3623,
"cdna_end": null,
"cdna_length": 6209,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 46,
"exon_rank_end": null,
"exon_count": 63,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.3301C>T",
"hgvs_p": "p.Pro1101Ser",
"transcript": "NM_080679.3",
"protein_id": "NP_542410.2",
"transcript_support_level": null,
"aa_start": 1101,
"aa_end": null,
"aa_length": 1629,
"cds_start": 3301,
"cds_end": null,
"cds_length": 4890,
"cdna_start": 3528,
"cdna_end": null,
"cdna_length": 6101,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.2776C>T",
"hgvs_p": "p.Pro926Ser",
"transcript": "NM_001424109.1",
"protein_id": "NP_001411038.1",
"transcript_support_level": null,
"aa_start": 926,
"aa_end": null,
"aa_length": 1454,
"cds_start": 2776,
"cds_end": null,
"cds_length": 4365,
"cdna_start": 3640,
"cdna_end": null,
"cdna_length": 6213,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 48,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.2596C>T",
"hgvs_p": "p.Pro866Ser",
"transcript": "NM_001424110.1",
"protein_id": "NP_001411039.1",
"transcript_support_level": null,
"aa_start": 866,
"aa_end": null,
"aa_length": 1394,
"cds_start": 2596,
"cds_end": null,
"cds_length": 4185,
"cdna_start": 3460,
"cdna_end": null,
"cdna_length": 6033,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 48,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.2596C>T",
"hgvs_p": "p.Pro866Ser",
"transcript": "NM_001424111.1",
"protein_id": "NP_001411040.1",
"transcript_support_level": null,
"aa_start": 866,
"aa_end": null,
"aa_length": 1394,
"cds_start": 2596,
"cds_end": null,
"cds_length": 4185,
"cdna_start": 3473,
"cdna_end": null,
"cdna_length": 6046,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.1576C>T",
"hgvs_p": "p.Pro526Ser",
"transcript": "NM_001424112.1",
"protein_id": "NP_001411041.1",
"transcript_support_level": null,
"aa_start": 526,
"aa_end": null,
"aa_length": 1054,
"cds_start": 1576,
"cds_end": null,
"cds_length": 3165,
"cdna_start": 1832,
"cdna_end": null,
"cdna_length": 4405,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 50,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.3622C>T",
"hgvs_p": "p.Pro1208Ser",
"transcript": "XM_017010250.2",
"protein_id": "XP_016865739.1",
"transcript_support_level": null,
"aa_start": 1208,
"aa_end": null,
"aa_length": 1736,
"cds_start": 3622,
"cds_end": null,
"cds_length": 5211,
"cdna_start": 4114,
"cdna_end": null,
"cdna_length": 6687,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.2908C>T",
"hgvs_p": "p.Pro970Ser",
"transcript": "XM_011514299.3",
"protein_id": "XP_011512601.1",
"transcript_support_level": null,
"aa_start": 970,
"aa_end": null,
"aa_length": 1498,
"cds_start": 2908,
"cds_end": null,
"cds_length": 4497,
"cdna_start": 3207,
"cdna_end": null,
"cdna_length": 5780,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.2776C>T",
"hgvs_p": "p.Pro926Ser",
"transcript": "XM_047418183.1",
"protein_id": "XP_047274139.1",
"transcript_support_level": null,
"aa_start": 926,
"aa_end": null,
"aa_length": 1454,
"cds_start": 2776,
"cds_end": null,
"cds_length": 4365,
"cdna_start": 3653,
"cdna_end": null,
"cdna_length": 6226,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 60,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.2728C>T",
"hgvs_p": "p.Pro910Ser",
"transcript": "XM_011514300.3",
"protein_id": "XP_011512602.1",
"transcript_support_level": null,
"aa_start": 910,
"aa_end": null,
"aa_length": 1438,
"cds_start": 2728,
"cds_end": null,
"cds_length": 4317,
"cdna_start": 3027,
"cdna_end": null,
"cdna_length": 5600,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.2509C>T",
"hgvs_p": "p.Pro837Ser",
"transcript": "XM_011514302.3",
"protein_id": "XP_011512604.1",
"transcript_support_level": null,
"aa_start": 837,
"aa_end": null,
"aa_length": 1365,
"cds_start": 2509,
"cds_end": null,
"cds_length": 4098,
"cdna_start": 3164,
"cdna_end": null,
"cdna_length": 5737,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "c.2440C>T",
"hgvs_p": "p.Pro814Ser",
"transcript": "XM_017010251.3",
"protein_id": "XP_016865740.1",
"transcript_support_level": null,
"aa_start": 814,
"aa_end": null,
"aa_length": 1342,
"cds_start": 2440,
"cds_end": null,
"cds_length": 4029,
"cdna_start": 2983,
"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": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"hgvs_c": "n.273-4245C>T",
"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
}
],
"gene_symbol": "COL11A2",
"gene_hgnc_id": 2187,
"dbsnp": "rs374515005",
"frequency_reference_population": 0.000056419554,
"hom_count_reference_population": 0,
"allele_count_reference_population": 91,
"gnomad_exomes_af": 0.0000506575,
"gnomad_genomes_af": 0.000111749,
"gnomad_exomes_ac": 74,
"gnomad_genomes_ac": 17,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.30328744649887085,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.529,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0736,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.02,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 0.61,
"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,BP6",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000341947.7",
"gene_symbol": "COL11A2",
"hgnc_id": 2187,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.3622C>T",
"hgvs_p": "p.Pro1208Ser"
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:1",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}