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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: X-50090127-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=50090127&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 50090127,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000376091.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.1756C>T",
"hgvs_p": "p.Arg586Trp",
"transcript": "NM_001127898.4",
"protein_id": "NP_001121370.1",
"transcript_support_level": null,
"aa_start": 586,
"aa_end": null,
"aa_length": 816,
"cds_start": 1756,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2157,
"cdna_end": null,
"cdna_length": 9863,
"mane_select": "ENST00000376091.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.1756C>T",
"hgvs_p": "p.Arg586Trp",
"transcript": "ENST00000376091.8",
"protein_id": "ENSP00000365259.3",
"transcript_support_level": 2,
"aa_start": 586,
"aa_end": null,
"aa_length": 816,
"cds_start": 1756,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2157,
"cdna_end": null,
"cdna_length": 9863,
"mane_select": "NM_001127898.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.1546C>T",
"hgvs_p": "p.Arg516Trp",
"transcript": "ENST00000307367.2",
"protein_id": "ENSP00000304257.2",
"transcript_support_level": 1,
"aa_start": 516,
"aa_end": null,
"aa_length": 746,
"cds_start": 1546,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 1837,
"cdna_end": null,
"cdna_length": 3177,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.1546C>T",
"hgvs_p": "p.Arg516Trp",
"transcript": "ENST00000376108.7",
"protein_id": "ENSP00000365276.3",
"transcript_support_level": 1,
"aa_start": 516,
"aa_end": null,
"aa_length": 746,
"cds_start": 1546,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 1778,
"cdna_end": null,
"cdna_length": 2660,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.1768C>T",
"hgvs_p": "p.Arg590Trp",
"transcript": "NM_001440756.1",
"protein_id": "NP_001427685.1",
"transcript_support_level": null,
"aa_start": 590,
"aa_end": null,
"aa_length": 820,
"cds_start": 1768,
"cds_end": null,
"cds_length": 2463,
"cdna_start": 2169,
"cdna_end": null,
"cdna_length": 9875,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.1768C>T",
"hgvs_p": "p.Arg590Trp",
"transcript": "NM_001440757.1",
"protein_id": "NP_001427686.1",
"transcript_support_level": null,
"aa_start": 590,
"aa_end": null,
"aa_length": 820,
"cds_start": 1768,
"cds_end": null,
"cds_length": 2463,
"cdna_start": 2428,
"cdna_end": null,
"cdna_length": 10134,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.1756C>T",
"hgvs_p": "p.Arg586Trp",
"transcript": "NM_001127899.4",
"protein_id": "NP_001121371.1",
"transcript_support_level": null,
"aa_start": 586,
"aa_end": null,
"aa_length": 816,
"cds_start": 1756,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2416,
"cdna_end": null,
"cdna_length": 10122,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.1756C>T",
"hgvs_p": "p.Arg586Trp",
"transcript": "ENST00000376088.7",
"protein_id": "ENSP00000365256.3",
"transcript_support_level": 2,
"aa_start": 586,
"aa_end": null,
"aa_length": 816,
"cds_start": 1756,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2397,
"cdna_end": null,
"cdna_length": 10108,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.1606C>T",
"hgvs_p": "p.Arg536Trp",
"transcript": "NM_001282163.2",
"protein_id": "NP_001269092.1",
"transcript_support_level": null,
"aa_start": 536,
"aa_end": null,
"aa_length": 766,
"cds_start": 1606,
"cds_end": null,
"cds_length": 2301,
"cdna_start": 1837,
"cdna_end": null,
"cdna_length": 9543,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.1546C>T",
"hgvs_p": "p.Arg516Trp",
"transcript": "NM_000084.5",
"protein_id": "NP_000075.1",
"transcript_support_level": null,
"aa_start": 516,
"aa_end": null,
"aa_length": 746,
"cds_start": 1546,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 1766,
"cdna_end": null,
"cdna_length": 9472,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.1546C>T",
"hgvs_p": "p.Arg516Trp",
"transcript": "ENST00000642885.1",
"protein_id": "ENSP00000496632.1",
"transcript_support_level": null,
"aa_start": 516,
"aa_end": null,
"aa_length": 746,
"cds_start": 1546,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 1698,
"cdna_end": null,
"cdna_length": 2834,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.1078C>T",
"hgvs_p": "p.Arg360Trp",
"transcript": "ENST00000642383.1",
"protein_id": "ENSP00000496353.1",
"transcript_support_level": null,
"aa_start": 360,
"aa_end": null,
"aa_length": 590,
"cds_start": 1078,
"cds_end": null,
"cds_length": 1773,
"cdna_start": 1078,
"cdna_end": null,
"cdna_length": 2214,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.1546C>T",
"hgvs_p": "p.Arg516Trp",
"transcript": "XM_047441807.1",
"protein_id": "XP_047297763.1",
"transcript_support_level": null,
"aa_start": 516,
"aa_end": null,
"aa_length": 746,
"cds_start": 1546,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 1808,
"cdna_end": null,
"cdna_length": 9514,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.1546C>T",
"hgvs_p": "p.Arg516Trp",
"transcript": "XM_047441808.1",
"protein_id": "XP_047297764.1",
"transcript_support_level": null,
"aa_start": 516,
"aa_end": null,
"aa_length": 746,
"cds_start": 1546,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 1863,
"cdna_end": null,
"cdna_length": 9569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "n.*1853C>T",
"hgvs_p": null,
"transcript": "ENST00000643129.1",
"protein_id": "ENSP00000496056.1",
"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": 3179,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "n.*931C>T",
"hgvs_p": null,
"transcript": "ENST00000646398.1",
"protein_id": "ENSP00000495122.1",
"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": 3470,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "n.2852C>T",
"hgvs_p": null,
"transcript": "NR_199781.1",
"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": 10558,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "n.*1853C>T",
"hgvs_p": null,
"transcript": "ENST00000643129.1",
"protein_id": "ENSP00000496056.1",
"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": 3179,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "n.*931C>T",
"hgvs_p": null,
"transcript": "ENST00000646398.1",
"protein_id": "ENSP00000495122.1",
"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": 3470,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"dbsnp": "rs797044812",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9883052110671997,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.94,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9843,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.68,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.405,
"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": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PM1",
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000376091.8",
"gene_symbol": "CLCN5",
"hgnc_id": 2023,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1756C>T",
"hgvs_p": "p.Arg586Trp"
}
],
"clinvar_disease": " X-linked recessive, low molecular weight, with hypercalciuria and nephrocalcinosis,Dent disease type 1,Hypophosphatemic rickets,Proteinuria,X-linked recessive nephrolithiasis with renal failure",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LP:2 O:1",
"phenotype_combined": "Dent disease type 1|X-linked recessive nephrolithiasis with renal failure;Dent disease type 1;Hypophosphatemic rickets, X-linked recessive;Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}