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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: 1-151813564-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=151813564&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 151813564,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000318247.7",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RORC",
"gene_hgnc_id": 10260,
"hgvs_c": "c.990C>T",
"hgvs_p": "p.Tyr330Tyr",
"transcript": "NM_005060.4",
"protein_id": "NP_005051.2",
"transcript_support_level": null,
"aa_start": 330,
"aa_end": null,
"aa_length": 518,
"cds_start": 990,
"cds_end": null,
"cds_length": 1557,
"cdna_start": 1028,
"cdna_end": null,
"cdna_length": 2996,
"mane_select": "ENST00000318247.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RORC",
"gene_hgnc_id": 10260,
"hgvs_c": "c.990C>T",
"hgvs_p": "p.Tyr330Tyr",
"transcript": "ENST00000318247.7",
"protein_id": "ENSP00000327025.6",
"transcript_support_level": 1,
"aa_start": 330,
"aa_end": null,
"aa_length": 518,
"cds_start": 990,
"cds_end": null,
"cds_length": 1557,
"cdna_start": 1028,
"cdna_end": null,
"cdna_length": 2996,
"mane_select": "NM_005060.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RORC",
"gene_hgnc_id": 10260,
"hgvs_c": "c.927C>T",
"hgvs_p": "p.Tyr309Tyr",
"transcript": "ENST00000356728.11",
"protein_id": "ENSP00000349164.6",
"transcript_support_level": 1,
"aa_start": 309,
"aa_end": null,
"aa_length": 497,
"cds_start": 927,
"cds_end": null,
"cds_length": 1494,
"cdna_start": 1087,
"cdna_end": null,
"cdna_length": 3055,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RORC",
"gene_hgnc_id": 10260,
"hgvs_c": "c.1009C>T",
"hgvs_p": "p.Arg337Cys",
"transcript": "XM_047427201.1",
"protein_id": "XP_047283157.1",
"transcript_support_level": null,
"aa_start": 337,
"aa_end": null,
"aa_length": 353,
"cds_start": 1009,
"cds_end": null,
"cds_length": 1062,
"cdna_start": 1169,
"cdna_end": null,
"cdna_length": 1245,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RORC",
"gene_hgnc_id": 10260,
"hgvs_c": "c.927C>T",
"hgvs_p": "p.Tyr309Tyr",
"transcript": "NM_001001523.2",
"protein_id": "NP_001001523.1",
"transcript_support_level": null,
"aa_start": 309,
"aa_end": null,
"aa_length": 497,
"cds_start": 927,
"cds_end": null,
"cds_length": 1494,
"cdna_start": 1087,
"cdna_end": null,
"cdna_length": 3055,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RORC",
"gene_hgnc_id": 10260,
"hgvs_c": "c.705C>T",
"hgvs_p": "p.Tyr235Tyr",
"transcript": "ENST00000652040.2",
"protein_id": "ENSP00000498548.2",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 423,
"cds_start": 705,
"cds_end": null,
"cds_length": 1272,
"cdna_start": 985,
"cdna_end": null,
"cdna_length": 2904,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RORC",
"gene_hgnc_id": 10260,
"hgvs_c": "c.1152C>T",
"hgvs_p": "p.Tyr384Tyr",
"transcript": "XM_006711484.5",
"protein_id": "XP_006711547.3",
"transcript_support_level": null,
"aa_start": 384,
"aa_end": null,
"aa_length": 572,
"cds_start": 1152,
"cds_end": null,
"cds_length": 1719,
"cdna_start": 1233,
"cdna_end": null,
"cdna_length": 3201,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RORC",
"gene_hgnc_id": 10260,
"hgvs_c": "n.1226C>T",
"hgvs_p": null,
"transcript": "ENST00000480719.1",
"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": 4141,
"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": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RORC",
"gene_hgnc_id": 10260,
"hgvs_c": "n.*1027C>T",
"hgvs_p": null,
"transcript": "ENST00000638901.1",
"protein_id": "ENSP00000492395.1",
"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": 2326,
"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": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RORC",
"gene_hgnc_id": 10260,
"hgvs_c": "n.1072C>T",
"hgvs_p": null,
"transcript": "ENST00000651814.1",
"protein_id": "ENSP00000498691.1",
"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": 3045,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RORC",
"gene_hgnc_id": 10260,
"hgvs_c": "n.128C>T",
"hgvs_p": null,
"transcript": "ENST00000697812.1",
"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": 1861,
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RORC",
"gene_hgnc_id": 10260,
"hgvs_c": "n.985C>T",
"hgvs_p": null,
"transcript": "ENST00000697813.1",
"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": 2005,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RORC",
"gene_hgnc_id": 10260,
"hgvs_c": "n.*1027C>T",
"hgvs_p": null,
"transcript": "ENST00000638901.1",
"protein_id": "ENSP00000492395.1",
"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": 2326,
"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": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "RORC",
"gene_hgnc_id": 10260,
"hgvs_c": "n.343-218C>T",
"hgvs_p": null,
"transcript": "ENST00000651893.1",
"protein_id": "ENSP00000498925.1",
"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": 2186,
"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": 8,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "RORC",
"gene_hgnc_id": 10260,
"hgvs_c": "n.933+1010C>T",
"hgvs_p": null,
"transcript": "ENST00000697811.1",
"protein_id": "ENSP00000513447.1",
"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": 2619,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RORC",
"gene_hgnc_id": 10260,
"dbsnp": "rs61754474",
"frequency_reference_population": 0.0022235329,
"hom_count_reference_population": 3,
"allele_count_reference_population": 3589,
"gnomad_exomes_af": 0.00227182,
"gnomad_genomes_af": 0.00176001,
"gnomad_exomes_ac": 3321,
"gnomad_genomes_ac": 268,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.4000000059604645,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.4,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.781,
"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": -19,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -19,
"benign_score": 19,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000318247.7",
"gene_symbol": "RORC",
"hgnc_id": 10260,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.990C>T",
"hgvs_p": "p.Tyr330Tyr"
}
],
"clinvar_disease": "Autosomal recessive mendelian susceptibility to mycobacterial diseases due to complete RORgamma receptor deficiency,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:2",
"phenotype_combined": "not provided|Autosomal recessive mendelian susceptibility to mycobacterial diseases due to complete RORgamma receptor deficiency",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}