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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: 17-58358524-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=58358524&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 58358524,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000407977.7",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF43",
"gene_hgnc_id": 18505,
"hgvs_c": "c.1252C>A",
"hgvs_p": "p.Leu418Met",
"transcript": "NM_017763.6",
"protein_id": "NP_060233.3",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 783,
"cds_start": 1252,
"cds_end": null,
"cds_length": 2352,
"cdna_start": 2155,
"cdna_end": null,
"cdna_length": 4522,
"mane_select": "ENST00000407977.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF43",
"gene_hgnc_id": 18505,
"hgvs_c": "c.1252C>A",
"hgvs_p": "p.Leu418Met",
"transcript": "ENST00000407977.7",
"protein_id": "ENSP00000385328.2",
"transcript_support_level": 2,
"aa_start": 418,
"aa_end": null,
"aa_length": 783,
"cds_start": 1252,
"cds_end": null,
"cds_length": 2352,
"cdna_start": 2155,
"cdna_end": null,
"cdna_length": 4522,
"mane_select": "NM_017763.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF43",
"gene_hgnc_id": 18505,
"hgvs_c": "c.1252C>A",
"hgvs_p": "p.Leu418Met",
"transcript": "ENST00000577716.5",
"protein_id": "ENSP00000462764.1",
"transcript_support_level": 1,
"aa_start": 418,
"aa_end": null,
"aa_length": 783,
"cds_start": 1252,
"cds_end": null,
"cds_length": 2352,
"cdna_start": 2000,
"cdna_end": null,
"cdna_length": 4367,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF43",
"gene_hgnc_id": 18505,
"hgvs_c": "c.1252C>A",
"hgvs_p": "p.Leu418Met",
"transcript": "ENST00000584437.5",
"protein_id": "ENSP00000463069.1",
"transcript_support_level": 1,
"aa_start": 418,
"aa_end": null,
"aa_length": 783,
"cds_start": 1252,
"cds_end": null,
"cds_length": 2352,
"cdna_start": 3208,
"cdna_end": null,
"cdna_length": 5575,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285897",
"gene_hgnc_id": null,
"hgvs_c": "n.1252C>A",
"hgvs_p": null,
"transcript": "ENST00000648873.1",
"protein_id": "ENSP00000497686.1",
"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": 5828,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF43",
"gene_hgnc_id": 18505,
"hgvs_c": "c.1252C>A",
"hgvs_p": "p.Leu418Met",
"transcript": "NM_001438820.1",
"protein_id": "NP_001425749.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 869,
"cds_start": 1252,
"cds_end": null,
"cds_length": 2610,
"cdna_start": 2069,
"cdna_end": null,
"cdna_length": 5394,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF43",
"gene_hgnc_id": 18505,
"hgvs_c": "c.1252C>A",
"hgvs_p": "p.Leu418Met",
"transcript": "NM_001438821.1",
"protein_id": "NP_001425750.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 869,
"cds_start": 1252,
"cds_end": null,
"cds_length": 2610,
"cdna_start": 3123,
"cdna_end": null,
"cdna_length": 6448,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF43",
"gene_hgnc_id": 18505,
"hgvs_c": "c.1252C>A",
"hgvs_p": "p.Leu418Met",
"transcript": "NM_001305544.3",
"protein_id": "NP_001292473.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 783,
"cds_start": 1252,
"cds_end": null,
"cds_length": 2352,
"cdna_start": 1952,
"cdna_end": null,
"cdna_length": 4319,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF43",
"gene_hgnc_id": 18505,
"hgvs_c": "c.1252C>A",
"hgvs_p": "p.Leu418Met",
"transcript": "NM_001438822.1",
"protein_id": "NP_001425751.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 783,
"cds_start": 1252,
"cds_end": null,
"cds_length": 2352,
"cdna_start": 3123,
"cdna_end": null,
"cdna_length": 5490,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF43",
"gene_hgnc_id": 18505,
"hgvs_c": "c.871C>A",
"hgvs_p": "p.Leu291Met",
"transcript": "NM_001437987.1",
"protein_id": "NP_001424916.1",
"transcript_support_level": null,
"aa_start": 291,
"aa_end": null,
"aa_length": 742,
"cds_start": 871,
"cds_end": null,
"cds_length": 2229,
"cdna_start": 1518,
"cdna_end": null,
"cdna_length": 4843,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF43",
"gene_hgnc_id": 18505,
"hgvs_c": "c.871C>A",
"hgvs_p": "p.Leu291Met",
"transcript": "ENST00000581868.1",
"protein_id": "ENSP00000462447.1",
"transcript_support_level": 2,
"aa_start": 291,
"aa_end": null,
"aa_length": 742,
"cds_start": 871,
"cds_end": null,
"cds_length": 2229,
"cdna_start": 1069,
"cdna_end": null,
"cdna_length": 2610,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF43",
"gene_hgnc_id": 18505,
"hgvs_c": "c.1129C>A",
"hgvs_p": "p.Leu377Met",
"transcript": "ENST00000583753.5",
"protein_id": "ENSP00000462502.1",
"transcript_support_level": 2,
"aa_start": 377,
"aa_end": null,
"aa_length": 742,
"cds_start": 1129,
"cds_end": null,
"cds_length": 2229,
"cdna_start": 1193,
"cdna_end": null,
"cdna_length": 3560,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF43",
"gene_hgnc_id": 18505,
"hgvs_c": "c.871C>A",
"hgvs_p": "p.Leu291Met",
"transcript": "NM_001305545.2",
"protein_id": "NP_001292474.1",
"transcript_support_level": null,
"aa_start": 291,
"aa_end": null,
"aa_length": 656,
"cds_start": 871,
"cds_end": null,
"cds_length": 1971,
"cdna_start": 1082,
"cdna_end": null,
"cdna_length": 3449,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF43",
"gene_hgnc_id": 18505,
"hgvs_c": "c.871C>A",
"hgvs_p": "p.Leu291Met",
"transcript": "ENST00000577625.5",
"protein_id": "ENSP00000463716.1",
"transcript_support_level": 2,
"aa_start": 291,
"aa_end": null,
"aa_length": 656,
"cds_start": 871,
"cds_end": null,
"cds_length": 1971,
"cdna_start": 1082,
"cdna_end": null,
"cdna_length": 2198,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF43",
"gene_hgnc_id": 18505,
"hgvs_c": "c.1252C>A",
"hgvs_p": "p.Leu418Met",
"transcript": "XM_047436332.1",
"protein_id": "XP_047292288.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 783,
"cds_start": 1252,
"cds_end": null,
"cds_length": 2352,
"cdna_start": 2069,
"cdna_end": null,
"cdna_length": 5612,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TSPOAP1-AS1",
"gene_hgnc_id": 44148,
"hgvs_c": "n.434+20845G>T",
"hgvs_p": null,
"transcript": "ENST00000583841.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 840,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RNF43",
"gene_hgnc_id": 18505,
"dbsnp": "rs2526374",
"frequency_reference_population": 0.37067774,
"hom_count_reference_population": 112612,
"allele_count_reference_population": 597878,
"gnomad_exomes_af": 0.369916,
"gnomad_genomes_af": 0.377992,
"gnomad_exomes_ac": 540390,
"gnomad_genomes_ac": 57488,
"gnomad_exomes_homalt": 101622,
"gnomad_genomes_homalt": 10990,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.00018858909606933594,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.106,
"revel_prediction": "Benign",
"alphamissense_score": 0.0971,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.64,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.487,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000407977.7",
"gene_symbol": "RNF43",
"hgnc_id": 18505,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1252C>A",
"hgvs_p": "p.Leu418Met"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000648873.1",
"gene_symbol": "ENSG00000285897",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1252C>A",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000583841.1",
"gene_symbol": "TSPOAP1-AS1",
"hgnc_id": 44148,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.434+20845G>T",
"hgvs_p": null
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}