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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: 5-95654363-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=95654363&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 95654363,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001131065.1",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFESD",
"gene_hgnc_id": 29587,
"hgvs_c": "c.365T>C",
"hgvs_p": "p.Ile122Thr",
"transcript": "NM_001131066.2",
"protein_id": "NP_001124538.1",
"transcript_support_level": null,
"aa_start": 122,
"aa_end": null,
"aa_length": 210,
"cds_start": 365,
"cds_end": null,
"cds_length": 633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000380005.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001131066.2"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFESD",
"gene_hgnc_id": 29587,
"hgvs_c": "c.365T>C",
"hgvs_p": "p.Ile122Thr",
"transcript": "ENST00000380005.9",
"protein_id": "ENSP00000369341.4",
"transcript_support_level": 2,
"aa_start": 122,
"aa_end": null,
"aa_length": 210,
"cds_start": 365,
"cds_end": null,
"cds_length": 633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001131066.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000380005.9"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFESD",
"gene_hgnc_id": 29587,
"hgvs_c": "c.206T>C",
"hgvs_p": "p.Ile69Thr",
"transcript": "ENST00000311364.9",
"protein_id": "ENSP00000309229.4",
"transcript_support_level": 1,
"aa_start": 69,
"aa_end": null,
"aa_length": 157,
"cds_start": 206,
"cds_end": null,
"cds_length": 474,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000311364.9"
},
{
"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": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SPATA9",
"gene_hgnc_id": 22988,
"hgvs_c": "n.*447+968A>G",
"hgvs_p": null,
"transcript": "ENST00000316087.12",
"protein_id": "ENSP00000325491.8",
"transcript_support_level": 1,
"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": "nonsense_mediated_decay",
"feature": "ENST00000316087.12"
},
{
"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": 7,
"intron_rank_end": null,
"gene_symbol": "SPATA9",
"gene_hgnc_id": 22988,
"hgvs_c": "n.1022+968A>G",
"hgvs_p": null,
"transcript": "ENST00000477047.6",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000477047.6"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFESD",
"gene_hgnc_id": 29587,
"hgvs_c": "c.365T>C",
"hgvs_p": "p.Ile122Thr",
"transcript": "NM_001131065.1",
"protein_id": "NP_001124537.1",
"transcript_support_level": null,
"aa_start": 122,
"aa_end": null,
"aa_length": 210,
"cds_start": 365,
"cds_end": null,
"cds_length": 633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001131065.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFESD",
"gene_hgnc_id": 29587,
"hgvs_c": "c.365T>C",
"hgvs_p": "p.Ile122Thr",
"transcript": "ENST00000458310.2",
"protein_id": "ENSP00000413592.1",
"transcript_support_level": 5,
"aa_start": 122,
"aa_end": null,
"aa_length": 210,
"cds_start": 365,
"cds_end": null,
"cds_length": 633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000458310.2"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFESD",
"gene_hgnc_id": 29587,
"hgvs_c": "c.365T>C",
"hgvs_p": "p.Ile122Thr",
"transcript": "ENST00000912998.1",
"protein_id": "ENSP00000583057.1",
"transcript_support_level": null,
"aa_start": 122,
"aa_end": null,
"aa_length": 210,
"cds_start": 365,
"cds_end": null,
"cds_length": 633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912998.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFESD",
"gene_hgnc_id": 29587,
"hgvs_c": "c.365T>C",
"hgvs_p": "p.Ile122Thr",
"transcript": "ENST00000912999.1",
"protein_id": "ENSP00000583058.1",
"transcript_support_level": null,
"aa_start": 122,
"aa_end": null,
"aa_length": 210,
"cds_start": 365,
"cds_end": null,
"cds_length": 633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912999.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFESD",
"gene_hgnc_id": 29587,
"hgvs_c": "c.206T>C",
"hgvs_p": "p.Ile69Thr",
"transcript": "NM_001375394.1",
"protein_id": "NP_001362323.1",
"transcript_support_level": null,
"aa_start": 69,
"aa_end": null,
"aa_length": 157,
"cds_start": 206,
"cds_end": null,
"cds_length": 474,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001375394.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFESD",
"gene_hgnc_id": 29587,
"hgvs_c": "c.206T>C",
"hgvs_p": "p.Ile69Thr",
"transcript": "NM_173362.3",
"protein_id": "NP_775498.1",
"transcript_support_level": null,
"aa_start": 69,
"aa_end": null,
"aa_length": 157,
"cds_start": 206,
"cds_end": null,
"cds_length": 474,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_173362.3"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFESD",
"gene_hgnc_id": 29587,
"hgvs_c": "c.206T>C",
"hgvs_p": "p.Ile69Thr",
"transcript": "ENST00000511684.6",
"protein_id": "ENSP00000422520.2",
"transcript_support_level": 3,
"aa_start": 69,
"aa_end": null,
"aa_length": 157,
"cds_start": 206,
"cds_end": null,
"cds_length": 474,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000511684.6"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFESD",
"gene_hgnc_id": 29587,
"hgvs_c": "c.365T>C",
"hgvs_p": "p.Ile122Thr",
"transcript": "XM_011543360.3",
"protein_id": "XP_011541662.1",
"transcript_support_level": null,
"aa_start": 122,
"aa_end": null,
"aa_length": 210,
"cds_start": 365,
"cds_end": null,
"cds_length": 633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011543360.3"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFESD",
"gene_hgnc_id": 29587,
"hgvs_c": "c.365T>C",
"hgvs_p": "p.Ile122Thr",
"transcript": "XM_017009413.2",
"protein_id": "XP_016864902.1",
"transcript_support_level": null,
"aa_start": 122,
"aa_end": null,
"aa_length": 210,
"cds_start": 365,
"cds_end": null,
"cds_length": 633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017009413.2"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFESD",
"gene_hgnc_id": 29587,
"hgvs_c": "c.206T>C",
"hgvs_p": "p.Ile69Thr",
"transcript": "XM_047417137.1",
"protein_id": "XP_047273093.1",
"transcript_support_level": null,
"aa_start": 69,
"aa_end": null,
"aa_length": 157,
"cds_start": 206,
"cds_end": null,
"cds_length": 474,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417137.1"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "RFESD",
"gene_hgnc_id": 29587,
"hgvs_c": "c.175+127T>C",
"hgvs_p": null,
"transcript": "ENST00000513950.2",
"protein_id": "ENSP00000425632.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 60,
"cds_start": null,
"cds_end": null,
"cds_length": 183,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000513950.2"
},
{
"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": 7,
"intron_rank_end": null,
"gene_symbol": "SPATA9",
"gene_hgnc_id": 22988,
"hgvs_c": "n.*447+968A>G",
"hgvs_p": null,
"transcript": "ENST00000477715.5",
"protein_id": "ENSP00000427257.1",
"transcript_support_level": 2,
"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": "nonsense_mediated_decay",
"feature": "ENST00000477715.5"
},
{
"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": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SPATA9",
"gene_hgnc_id": 22988,
"hgvs_c": "n.1349+968A>G",
"hgvs_p": null,
"transcript": "NR_125327.2",
"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": "NR_125327.2"
},
{
"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": 7,
"intron_rank_end": null,
"gene_symbol": "SPATA9",
"gene_hgnc_id": 22988,
"hgvs_c": "n.1041+968A>G",
"hgvs_p": null,
"transcript": "NR_125328.1",
"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": "NR_125328.1"
},
{
"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": 7,
"intron_rank_end": null,
"gene_symbol": "SPATA9",
"gene_hgnc_id": 22988,
"hgvs_c": "n.1121+968A>G",
"hgvs_p": null,
"transcript": "NR_125330.2",
"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": "NR_125330.2"
},
{
"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": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "SPATA9",
"gene_hgnc_id": 22988,
"hgvs_c": "n.1073+968A>G",
"hgvs_p": null,
"transcript": "XR_001742295.1",
"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_001742295.1"
}
],
"gene_symbol": "RFESD",
"gene_hgnc_id": 29587,
"dbsnp": "rs200861427",
"frequency_reference_population": 0.000015106101,
"hom_count_reference_population": 0,
"allele_count_reference_population": 24,
"gnomad_exomes_af": 0.00000556877,
"gnomad_genomes_af": 0.00010514,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": 16,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6704592704772949,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.64,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.466,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.39,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.046,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.02,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "NM_001131065.1",
"gene_symbol": "RFESD",
"hgnc_id": 29587,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.365T>C",
"hgvs_p": "p.Ile122Thr"
},
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000316087.12",
"gene_symbol": "SPATA9",
"hgnc_id": 22988,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.*447+968A>G",
"hgvs_p": null
}
],
"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
}