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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: 19-13799870-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=13799870&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 13799870,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001367834.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZSWIM4",
"gene_hgnc_id": 25704,
"hgvs_c": "c.304C>T",
"hgvs_p": "p.Arg102Cys",
"transcript": "NM_001367834.3",
"protein_id": "NP_001354763.1",
"transcript_support_level": null,
"aa_start": 102,
"aa_end": null,
"aa_length": 1106,
"cds_start": 304,
"cds_end": null,
"cds_length": 3321,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000590508.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001367834.3"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZSWIM4",
"gene_hgnc_id": 25704,
"hgvs_c": "c.304C>T",
"hgvs_p": "p.Arg102Cys",
"transcript": "ENST00000590508.6",
"protein_id": "ENSP00000468285.2",
"transcript_support_level": 2,
"aa_start": 102,
"aa_end": null,
"aa_length": 1106,
"cds_start": 304,
"cds_end": null,
"cds_length": 3321,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001367834.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000590508.6"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZSWIM4",
"gene_hgnc_id": 25704,
"hgvs_c": "c.352C>T",
"hgvs_p": "p.Arg118Cys",
"transcript": "ENST00000938264.1",
"protein_id": "ENSP00000608323.1",
"transcript_support_level": null,
"aa_start": 118,
"aa_end": null,
"aa_length": 1122,
"cds_start": 352,
"cds_end": null,
"cds_length": 3369,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938264.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZSWIM4",
"gene_hgnc_id": 25704,
"hgvs_c": "c.304C>T",
"hgvs_p": "p.Arg102Cys",
"transcript": "ENST00000938266.1",
"protein_id": "ENSP00000608325.1",
"transcript_support_level": null,
"aa_start": 102,
"aa_end": null,
"aa_length": 1083,
"cds_start": 304,
"cds_end": null,
"cds_length": 3252,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938266.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZSWIM4",
"gene_hgnc_id": 25704,
"hgvs_c": "c.304C>T",
"hgvs_p": "p.Arg102Cys",
"transcript": "NM_023072.3",
"protein_id": "NP_075560.2",
"transcript_support_level": null,
"aa_start": 102,
"aa_end": null,
"aa_length": 989,
"cds_start": 304,
"cds_end": null,
"cds_length": 2970,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_023072.3"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZSWIM4",
"gene_hgnc_id": 25704,
"hgvs_c": "c.304C>T",
"hgvs_p": "p.Arg102Cys",
"transcript": "ENST00000254323.6",
"protein_id": "ENSP00000254323.2",
"transcript_support_level": 2,
"aa_start": 102,
"aa_end": null,
"aa_length": 989,
"cds_start": 304,
"cds_end": null,
"cds_length": 2970,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000254323.6"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZSWIM4",
"gene_hgnc_id": 25704,
"hgvs_c": "c.304C>T",
"hgvs_p": "p.Arg102Cys",
"transcript": "ENST00000938263.1",
"protein_id": "ENSP00000608322.1",
"transcript_support_level": null,
"aa_start": 102,
"aa_end": null,
"aa_length": 933,
"cds_start": 304,
"cds_end": null,
"cds_length": 2802,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938263.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZSWIM4",
"gene_hgnc_id": 25704,
"hgvs_c": "c.304C>T",
"hgvs_p": "p.Arg102Cys",
"transcript": "ENST00000938265.1",
"protein_id": "ENSP00000608324.1",
"transcript_support_level": null,
"aa_start": 102,
"aa_end": null,
"aa_length": 892,
"cds_start": 304,
"cds_end": null,
"cds_length": 2679,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938265.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZSWIM4",
"gene_hgnc_id": 25704,
"hgvs_c": "c.304C>T",
"hgvs_p": "p.Arg102Cys",
"transcript": "XM_017027153.2",
"protein_id": "XP_016882642.1",
"transcript_support_level": null,
"aa_start": 102,
"aa_end": null,
"aa_length": 1122,
"cds_start": 304,
"cds_end": null,
"cds_length": 3369,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017027153.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZSWIM4",
"gene_hgnc_id": 25704,
"hgvs_c": "c.304C>T",
"hgvs_p": "p.Arg102Cys",
"transcript": "XM_017027154.2",
"protein_id": "XP_016882643.1",
"transcript_support_level": null,
"aa_start": 102,
"aa_end": null,
"aa_length": 1099,
"cds_start": 304,
"cds_end": null,
"cds_length": 3300,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017027154.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZSWIM4",
"gene_hgnc_id": 25704,
"hgvs_c": "c.304C>T",
"hgvs_p": "p.Arg102Cys",
"transcript": "XM_017027155.2",
"protein_id": "XP_016882644.1",
"transcript_support_level": null,
"aa_start": 102,
"aa_end": null,
"aa_length": 1066,
"cds_start": 304,
"cds_end": null,
"cds_length": 3201,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017027155.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZSWIM4",
"gene_hgnc_id": 25704,
"hgvs_c": "c.304C>T",
"hgvs_p": "p.Arg102Cys",
"transcript": "XM_047439235.1",
"protein_id": "XP_047295191.1",
"transcript_support_level": null,
"aa_start": 102,
"aa_end": null,
"aa_length": 1050,
"cds_start": 304,
"cds_end": null,
"cds_length": 3153,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047439235.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZSWIM4",
"gene_hgnc_id": 25704,
"hgvs_c": "c.64C>T",
"hgvs_p": "p.Arg22Cys",
"transcript": "XM_024451657.2",
"protein_id": "XP_024307425.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 1042,
"cds_start": 64,
"cds_end": null,
"cds_length": 3129,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024451657.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZSWIM4",
"gene_hgnc_id": 25704,
"hgvs_c": "c.304C>T",
"hgvs_p": "p.Arg102Cys",
"transcript": "XM_047439236.1",
"protein_id": "XP_047295192.1",
"transcript_support_level": null,
"aa_start": 102,
"aa_end": null,
"aa_length": 1028,
"cds_start": 304,
"cds_end": null,
"cds_length": 3087,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047439236.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZSWIM4",
"gene_hgnc_id": 25704,
"hgvs_c": "c.304C>T",
"hgvs_p": "p.Arg102Cys",
"transcript": "XM_017027157.2",
"protein_id": "XP_016882646.1",
"transcript_support_level": null,
"aa_start": 102,
"aa_end": null,
"aa_length": 726,
"cds_start": 304,
"cds_end": null,
"cds_length": 2181,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017027157.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ZSWIM4",
"gene_hgnc_id": 25704,
"hgvs_c": "c.-228+4069C>T",
"hgvs_p": null,
"transcript": "XM_017027156.2",
"protein_id": "XP_016882645.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 928,
"cds_start": null,
"cds_end": null,
"cds_length": 2787,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017027156.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ZSWIM4",
"gene_hgnc_id": 25704,
"hgvs_c": "c.-228+4069C>T",
"hgvs_p": null,
"transcript": "XM_047439237.1",
"protein_id": "XP_047295193.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 912,
"cds_start": null,
"cds_end": null,
"cds_length": 2739,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047439237.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZSWIM4",
"gene_hgnc_id": 25704,
"hgvs_c": "n.510C>T",
"hgvs_p": null,
"transcript": "XR_007066949.1",
"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": "XR_007066949.1"
}
],
"gene_symbol": "ZSWIM4",
"gene_hgnc_id": 25704,
"dbsnp": "rs369720289",
"frequency_reference_population": 0.00007066376,
"hom_count_reference_population": 0,
"allele_count_reference_population": 114,
"gnomad_exomes_af": 0.0000732317,
"gnomad_genomes_af": 0.0000460048,
"gnomad_exomes_ac": 107,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8238793611526489,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.407,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3492,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.11,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.058,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001367834.3",
"gene_symbol": "ZSWIM4",
"hgnc_id": 25704,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.304C>T",
"hgvs_p": "p.Arg102Cys"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}