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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: 1-102888582-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=102888582&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 102888582,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_080629.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 62,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A1",
"gene_hgnc_id": 2186,
"hgvs_c": "c.4603T>C",
"hgvs_p": "p.Ser1535Pro",
"transcript": "NM_001854.4",
"protein_id": "NP_001845.3",
"transcript_support_level": null,
"aa_start": 1535,
"aa_end": null,
"aa_length": 1806,
"cds_start": 4603,
"cds_end": null,
"cds_length": 5421,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000370096.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001854.4"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 62,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A1",
"gene_hgnc_id": 2186,
"hgvs_c": "c.4603T>C",
"hgvs_p": "p.Ser1535Pro",
"transcript": "ENST00000370096.9",
"protein_id": "ENSP00000359114.3",
"transcript_support_level": 1,
"aa_start": 1535,
"aa_end": null,
"aa_length": 1806,
"cds_start": 4603,
"cds_end": null,
"cds_length": 5421,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001854.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370096.9"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 60,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A1",
"gene_hgnc_id": 2186,
"hgvs_c": "c.4255T>C",
"hgvs_p": "p.Ser1419Pro",
"transcript": "ENST00000512756.5",
"protein_id": "ENSP00000426533.1",
"transcript_support_level": 1,
"aa_start": 1419,
"aa_end": null,
"aa_length": 1690,
"cds_start": 4255,
"cds_end": null,
"cds_length": 5073,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000512756.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 59,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A1",
"gene_hgnc_id": 2186,
"hgvs_c": "n.*1853T>C",
"hgvs_p": null,
"transcript": "ENST00000635193.1",
"protein_id": "ENSP00000489428.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000635193.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 59,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A1",
"gene_hgnc_id": 2186,
"hgvs_c": "n.*1853T>C",
"hgvs_p": null,
"transcript": "ENST00000635193.1",
"protein_id": "ENSP00000489428.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000635193.1"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 62,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A1",
"gene_hgnc_id": 2186,
"hgvs_c": "c.4639T>C",
"hgvs_p": "p.Ser1547Pro",
"transcript": "NM_080629.3",
"protein_id": "NP_542196.2",
"transcript_support_level": null,
"aa_start": 1547,
"aa_end": null,
"aa_length": 1818,
"cds_start": 4639,
"cds_end": null,
"cds_length": 5457,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_080629.3"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 62,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A1",
"gene_hgnc_id": 2186,
"hgvs_c": "c.4639T>C",
"hgvs_p": "p.Ser1547Pro",
"transcript": "ENST00000358392.6",
"protein_id": "ENSP00000351163.2",
"transcript_support_level": 5,
"aa_start": 1547,
"aa_end": null,
"aa_length": 1818,
"cds_start": 4639,
"cds_end": null,
"cds_length": 5457,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000358392.6"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 61,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A1",
"gene_hgnc_id": 2186,
"hgvs_c": "c.4549T>C",
"hgvs_p": "p.Ser1517Pro",
"transcript": "ENST00000862751.1",
"protein_id": "ENSP00000532810.1",
"transcript_support_level": null,
"aa_start": 1517,
"aa_end": null,
"aa_length": 1788,
"cds_start": 4549,
"cds_end": null,
"cds_length": 5367,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862751.1"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 61,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A1",
"gene_hgnc_id": 2186,
"hgvs_c": "c.4486T>C",
"hgvs_p": "p.Ser1496Pro",
"transcript": "NM_001190709.2",
"protein_id": "NP_001177638.1",
"transcript_support_level": null,
"aa_start": 1496,
"aa_end": null,
"aa_length": 1767,
"cds_start": 4486,
"cds_end": null,
"cds_length": 5304,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001190709.2"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 61,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A1",
"gene_hgnc_id": 2186,
"hgvs_c": "c.4486T>C",
"hgvs_p": "p.Ser1496Pro",
"transcript": "ENST00000353414.8",
"protein_id": "ENSP00000302551.6",
"transcript_support_level": 5,
"aa_start": 1496,
"aa_end": null,
"aa_length": 1767,
"cds_start": 4486,
"cds_end": null,
"cds_length": 5304,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000353414.8"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 61,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A1",
"gene_hgnc_id": 2186,
"hgvs_c": "c.4348T>C",
"hgvs_p": "p.Ser1450Pro",
"transcript": "ENST00000918009.1",
"protein_id": "ENSP00000588068.1",
"transcript_support_level": null,
"aa_start": 1450,
"aa_end": null,
"aa_length": 1721,
"cds_start": 4348,
"cds_end": null,
"cds_length": 5166,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918009.1"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 60,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A1",
"gene_hgnc_id": 2186,
"hgvs_c": "c.4255T>C",
"hgvs_p": "p.Ser1419Pro",
"transcript": "NM_080630.4",
"protein_id": "NP_542197.3",
"transcript_support_level": null,
"aa_start": 1419,
"aa_end": null,
"aa_length": 1690,
"cds_start": 4255,
"cds_end": null,
"cds_length": 5073,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_080630.4"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 63,
"exon_rank_end": null,
"exon_count": 68,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A1",
"gene_hgnc_id": 2186,
"hgvs_c": "c.4756T>C",
"hgvs_p": "p.Ser1586Pro",
"transcript": "XM_017000334.2",
"protein_id": "XP_016855823.1",
"transcript_support_level": null,
"aa_start": 1586,
"aa_end": null,
"aa_length": 1857,
"cds_start": 4756,
"cds_end": null,
"cds_length": 5574,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000334.2"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 63,
"exon_rank_end": null,
"exon_count": 68,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A1",
"gene_hgnc_id": 2186,
"hgvs_c": "c.4750T>C",
"hgvs_p": "p.Ser1584Pro",
"transcript": "XM_017000335.2",
"protein_id": "XP_016855824.1",
"transcript_support_level": null,
"aa_start": 1584,
"aa_end": null,
"aa_length": 1855,
"cds_start": 4750,
"cds_end": null,
"cds_length": 5568,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000335.2"
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 53,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A1",
"gene_hgnc_id": 2186,
"hgvs_c": "c.3154T>C",
"hgvs_p": "p.Ser1052Pro",
"transcript": "XM_017000337.2",
"protein_id": "XP_016855826.1",
"transcript_support_level": null,
"aa_start": 1052,
"aa_end": null,
"aa_length": 1323,
"cds_start": 3154,
"cds_end": null,
"cds_length": 3972,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000337.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 63,
"exon_rank_end": null,
"exon_count": 68,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL11A1",
"gene_hgnc_id": 2186,
"hgvs_c": "n.4963T>C",
"hgvs_p": null,
"transcript": "NR_134980.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_134980.2"
}
],
"gene_symbol": "COL11A1",
"gene_hgnc_id": 2186,
"dbsnp": "rs1676486",
"frequency_reference_population": 0.8017561,
"hom_count_reference_population": 519995,
"allele_count_reference_population": 1292628,
"gnomad_exomes_af": 0.800675,
"gnomad_genomes_af": 0.81213,
"gnomad_exomes_ac": 1169051,
"gnomad_genomes_ac": 123577,
"gnomad_exomes_homalt": 469728,
"gnomad_genomes_homalt": 50267,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0000012520566770035657,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.318,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0472,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.21,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.474,
"phylop100way_prediction": "Uncertain_significance",
"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": -18,
"acmg_classification": "Benign",
"acmg_criteria": "PM1,BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -18,
"benign_score": 20,
"pathogenic_score": 2,
"criteria": [
"PM1",
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_080629.3",
"gene_symbol": "COL11A1",
"hgnc_id": 2186,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.4639T>C",
"hgvs_p": "p.Ser1547Pro"
}
],
"clinvar_disease": " autosomal dominant 37, susceptibility to,Connective tissue disorder,Fibrochondrogenesis 1,Hearing loss,Lumbar disk herniation,Marshall syndrome,Stickler syndrome type 2,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:12",
"phenotype_combined": "Hearing loss, autosomal dominant 37|not provided|Marshall syndrome|Stickler syndrome type 2|Fibrochondrogenesis 1|not specified|Lumbar disk herniation, susceptibility to|Connective tissue disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}