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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-50090846-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=50090846&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 50090846,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000376091.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.2320C>T",
"hgvs_p": "p.Arg774*",
"transcript": "NM_001127898.4",
"protein_id": "NP_001121370.1",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 816,
"cds_start": 2320,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2721,
"cdna_end": null,
"cdna_length": 9863,
"mane_select": "ENST00000376091.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.2320C>T",
"hgvs_p": "p.Arg774*",
"transcript": "ENST00000376091.8",
"protein_id": "ENSP00000365259.3",
"transcript_support_level": 2,
"aa_start": 774,
"aa_end": null,
"aa_length": 816,
"cds_start": 2320,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2721,
"cdna_end": null,
"cdna_length": 9863,
"mane_select": "NM_001127898.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.2110C>T",
"hgvs_p": "p.Arg704*",
"transcript": "ENST00000307367.2",
"protein_id": "ENSP00000304257.2",
"transcript_support_level": 1,
"aa_start": 704,
"aa_end": null,
"aa_length": 746,
"cds_start": 2110,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 2401,
"cdna_end": null,
"cdna_length": 3177,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.2110C>T",
"hgvs_p": "p.Arg704*",
"transcript": "ENST00000376108.7",
"protein_id": "ENSP00000365276.3",
"transcript_support_level": 1,
"aa_start": 704,
"aa_end": null,
"aa_length": 746,
"cds_start": 2110,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 2342,
"cdna_end": null,
"cdna_length": 2660,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.2332C>T",
"hgvs_p": "p.Arg778*",
"transcript": "NM_001440756.1",
"protein_id": "NP_001427685.1",
"transcript_support_level": null,
"aa_start": 778,
"aa_end": null,
"aa_length": 820,
"cds_start": 2332,
"cds_end": null,
"cds_length": 2463,
"cdna_start": 2733,
"cdna_end": null,
"cdna_length": 9875,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.2332C>T",
"hgvs_p": "p.Arg778*",
"transcript": "NM_001440757.1",
"protein_id": "NP_001427686.1",
"transcript_support_level": null,
"aa_start": 778,
"aa_end": null,
"aa_length": 820,
"cds_start": 2332,
"cds_end": null,
"cds_length": 2463,
"cdna_start": 2992,
"cdna_end": null,
"cdna_length": 10134,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.2320C>T",
"hgvs_p": "p.Arg774*",
"transcript": "NM_001127899.4",
"protein_id": "NP_001121371.1",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 816,
"cds_start": 2320,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2980,
"cdna_end": null,
"cdna_length": 10122,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.2320C>T",
"hgvs_p": "p.Arg774*",
"transcript": "ENST00000376088.7",
"protein_id": "ENSP00000365256.3",
"transcript_support_level": 2,
"aa_start": 774,
"aa_end": null,
"aa_length": 816,
"cds_start": 2320,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2961,
"cdna_end": null,
"cdna_length": 10108,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.2170C>T",
"hgvs_p": "p.Arg724*",
"transcript": "NM_001282163.2",
"protein_id": "NP_001269092.1",
"transcript_support_level": null,
"aa_start": 724,
"aa_end": null,
"aa_length": 766,
"cds_start": 2170,
"cds_end": null,
"cds_length": 2301,
"cdna_start": 2401,
"cdna_end": null,
"cdna_length": 9543,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.2110C>T",
"hgvs_p": "p.Arg704*",
"transcript": "NM_000084.5",
"protein_id": "NP_000075.1",
"transcript_support_level": null,
"aa_start": 704,
"aa_end": null,
"aa_length": 746,
"cds_start": 2110,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 2330,
"cdna_end": null,
"cdna_length": 9472,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.2110C>T",
"hgvs_p": "p.Arg704*",
"transcript": "ENST00000642885.1",
"protein_id": "ENSP00000496632.1",
"transcript_support_level": null,
"aa_start": 704,
"aa_end": null,
"aa_length": 746,
"cds_start": 2110,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 2262,
"cdna_end": null,
"cdna_length": 2834,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.1642C>T",
"hgvs_p": "p.Arg548*",
"transcript": "ENST00000642383.1",
"protein_id": "ENSP00000496353.1",
"transcript_support_level": null,
"aa_start": 548,
"aa_end": null,
"aa_length": 590,
"cds_start": 1642,
"cds_end": null,
"cds_length": 1773,
"cdna_start": 1642,
"cdna_end": null,
"cdna_length": 2214,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.2110C>T",
"hgvs_p": "p.Arg704*",
"transcript": "XM_047441807.1",
"protein_id": "XP_047297763.1",
"transcript_support_level": null,
"aa_start": 704,
"aa_end": null,
"aa_length": 746,
"cds_start": 2110,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 2372,
"cdna_end": null,
"cdna_length": 9514,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "c.2110C>T",
"hgvs_p": "p.Arg704*",
"transcript": "XM_047441808.1",
"protein_id": "XP_047297764.1",
"transcript_support_level": null,
"aa_start": 704,
"aa_end": null,
"aa_length": 746,
"cds_start": 2110,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 2427,
"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": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "n.*2417C>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": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "n.*1495C>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": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "n.3416C>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": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "n.*2417C>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": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN5",
"gene_hgnc_id": 2023,
"hgvs_c": "n.*1495C>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": "rs151340624",
"frequency_reference_population": 0.000002732661,
"hom_count_reference_population": 1,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000273266,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6200000047683716,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.62,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.898,
"phylop100way_prediction": "Uncertain_significance",
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PVS1_Moderate,PM2,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PVS1_Moderate",
"PM2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000376091.8",
"gene_symbol": "CLCN5",
"hgnc_id": 2023,
"effects": [
"stop_gained"
],
"inheritance_mode": "XL",
"hgvs_c": "c.2320C>T",
"hgvs_p": "p.Arg774*"
}
],
"clinvar_disease": " low molecular weight, with hypercalciuria and nephrocalcinosis,CLCN5-related disorder,Dent disease type 1,Proteinuria,X-linked recessive nephrolithiasis with renal failure",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:1",
"phenotype_combined": "X-linked recessive nephrolithiasis with renal failure|CLCN5-related disorder|Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis;Dent disease type 1",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}