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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: 10-12172866-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=12172866&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 12172866,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_014142.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.386C>T",
"hgvs_p": "p.Ala129Val",
"transcript": "NM_014142.4",
"protein_id": "NP_054861.2",
"transcript_support_level": null,
"aa_start": 129,
"aa_end": null,
"aa_length": 219,
"cds_start": 386,
"cds_end": null,
"cds_length": 660,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000491614.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_014142.4"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.386C>T",
"hgvs_p": "p.Ala129Val",
"transcript": "ENST00000491614.6",
"protein_id": "ENSP00000419628.1",
"transcript_support_level": 1,
"aa_start": 129,
"aa_end": null,
"aa_length": 219,
"cds_start": 386,
"cds_end": null,
"cds_length": 660,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_014142.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000491614.6"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.425C>T",
"hgvs_p": "p.Ala142Val",
"transcript": "ENST00000378937.7",
"protein_id": "ENSP00000368219.3",
"transcript_support_level": 3,
"aa_start": 142,
"aa_end": null,
"aa_length": 232,
"cds_start": 425,
"cds_end": null,
"cds_length": 699,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000378937.7"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.386C>T",
"hgvs_p": "p.Ala129Val",
"transcript": "ENST00000905393.1",
"protein_id": "ENSP00000575452.1",
"transcript_support_level": null,
"aa_start": 129,
"aa_end": null,
"aa_length": 231,
"cds_start": 386,
"cds_end": null,
"cds_length": 696,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905393.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.386C>T",
"hgvs_p": "p.Ala129Val",
"transcript": "NM_001321647.2",
"protein_id": "NP_001308576.1",
"transcript_support_level": null,
"aa_start": 129,
"aa_end": null,
"aa_length": 216,
"cds_start": 386,
"cds_end": null,
"cds_length": 651,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001321647.2"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.386C>T",
"hgvs_p": "p.Ala129Val",
"transcript": "ENST00000905392.1",
"protein_id": "ENSP00000575451.1",
"transcript_support_level": null,
"aa_start": 129,
"aa_end": null,
"aa_length": 216,
"cds_start": 386,
"cds_end": null,
"cds_length": 651,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905392.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.386C>T",
"hgvs_p": "p.Ala129Val",
"transcript": "ENST00000905394.1",
"protein_id": "ENSP00000575453.1",
"transcript_support_level": null,
"aa_start": 129,
"aa_end": null,
"aa_length": 216,
"cds_start": 386,
"cds_end": null,
"cds_length": 651,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905394.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.386C>T",
"hgvs_p": "p.Ala129Val",
"transcript": "ENST00000378940.7",
"protein_id": "ENSP00000368222.3",
"transcript_support_level": 5,
"aa_start": 129,
"aa_end": null,
"aa_length": 186,
"cds_start": 386,
"cds_end": null,
"cds_length": 561,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000378940.7"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.290C>T",
"hgvs_p": "p.Ala97Val",
"transcript": "ENST00000905395.1",
"protein_id": "ENSP00000575454.1",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 184,
"cds_start": 290,
"cds_end": null,
"cds_length": 555,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905395.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.386C>T",
"hgvs_p": "p.Ala129Val",
"transcript": "ENST00000378927.7",
"protein_id": "ENSP00000368209.3",
"transcript_support_level": 2,
"aa_start": 129,
"aa_end": null,
"aa_length": 180,
"cds_start": 386,
"cds_end": null,
"cds_length": 543,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000378927.7"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.128C>T",
"hgvs_p": "p.Ala43Val",
"transcript": "NM_001321648.2",
"protein_id": "NP_001308577.1",
"transcript_support_level": null,
"aa_start": 43,
"aa_end": null,
"aa_length": 133,
"cds_start": 128,
"cds_end": null,
"cds_length": 402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001321648.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "n.613C>T",
"hgvs_p": null,
"transcript": "ENST00000378952.7",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000378952.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "n.254C>T",
"hgvs_p": null,
"transcript": "ENST00000476462.5",
"protein_id": "ENSP00000436844.1",
"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": "ENST00000476462.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "n.97C>T",
"hgvs_p": null,
"transcript": "ENST00000498825.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000498825.1"
}
],
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"dbsnp": "rs146519172",
"frequency_reference_population": 0.000057830137,
"hom_count_reference_population": 0,
"allele_count_reference_population": 93,
"gnomad_exomes_af": 0.0000494578,
"gnomad_genomes_af": 0.000137822,
"gnomad_exomes_ac": 72,
"gnomad_genomes_ac": 21,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.05838772654533386,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07199999690055847,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.029,
"revel_prediction": "Benign",
"alphamissense_score": 0.1138,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.6,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.482,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000121209429040229,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_014142.4",
"gene_symbol": "NUDT5",
"hgnc_id": 8052,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.386C>T",
"hgvs_p": "p.Ala129Val"
}
],
"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
}