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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: 10-12177821-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=12177821&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 12177821,
"ref": "C",
"alt": "T",
"effect": "start_lost",
"transcript": "NM_001321648.2",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.261G>A",
"hgvs_p": "p.Met87Ile",
"transcript": "NM_014142.4",
"protein_id": "NP_054861.2",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 219,
"cds_start": 261,
"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": "M",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.261G>A",
"hgvs_p": "p.Met87Ile",
"transcript": "ENST00000491614.6",
"protein_id": "ENSP00000419628.1",
"transcript_support_level": 1,
"aa_start": 87,
"aa_end": null,
"aa_length": 219,
"cds_start": 261,
"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": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.3G>A",
"hgvs_p": "p.Met1?",
"transcript": "NM_001321648.2",
"protein_id": "NP_001308577.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 133,
"cds_start": 3,
"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": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.300G>A",
"hgvs_p": "p.Met100Ile",
"transcript": "ENST00000378937.7",
"protein_id": "ENSP00000368219.3",
"transcript_support_level": 3,
"aa_start": 100,
"aa_end": null,
"aa_length": 232,
"cds_start": 300,
"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": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.261G>A",
"hgvs_p": "p.Met87Ile",
"transcript": "ENST00000905393.1",
"protein_id": "ENSP00000575452.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 231,
"cds_start": 261,
"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": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.261G>A",
"hgvs_p": "p.Met87Ile",
"transcript": "NM_001321647.2",
"protein_id": "NP_001308576.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 216,
"cds_start": 261,
"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": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.261G>A",
"hgvs_p": "p.Met87Ile",
"transcript": "ENST00000905392.1",
"protein_id": "ENSP00000575451.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 216,
"cds_start": 261,
"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": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.261G>A",
"hgvs_p": "p.Met87Ile",
"transcript": "ENST00000905394.1",
"protein_id": "ENSP00000575453.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 216,
"cds_start": 261,
"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": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.261G>A",
"hgvs_p": "p.Met87Ile",
"transcript": "ENST00000378940.7",
"protein_id": "ENSP00000368222.3",
"transcript_support_level": 5,
"aa_start": 87,
"aa_end": null,
"aa_length": 186,
"cds_start": 261,
"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": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.261G>A",
"hgvs_p": "p.Met87Ile",
"transcript": "ENST00000905395.1",
"protein_id": "ENSP00000575454.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 184,
"cds_start": 261,
"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": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.261G>A",
"hgvs_p": "p.Met87Ile",
"transcript": "ENST00000378927.7",
"protein_id": "ENSP00000368209.3",
"transcript_support_level": 2,
"aa_start": 87,
"aa_end": null,
"aa_length": 180,
"cds_start": 261,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "n.488G>A",
"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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "n.129G>A",
"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": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"hgvs_c": "c.*22G>A",
"hgvs_p": null,
"transcript": "ENST00000444732.1",
"protein_id": "ENSP00000407856.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 96,
"cds_start": null,
"cds_end": null,
"cds_length": 293,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000444732.1"
}
],
"gene_symbol": "NUDT5",
"gene_hgnc_id": 8052,
"dbsnp": "rs149162963",
"frequency_reference_population": 0.000002052301,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.0000020523,
"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": 0.09136426448822021,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.037,
"revel_prediction": "Benign",
"alphamissense_score": 0.3946,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.47,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.559,
"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": "PVS1_Supporting,PM2",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PVS1_Supporting",
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001321648.2",
"gene_symbol": "NUDT5",
"hgnc_id": 8052,
"effects": [
"start_lost"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3G>A",
"hgvs_p": "p.Met1?"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}