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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: 5-140647913-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=140647913&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 140647913,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_006083.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IK",
"gene_hgnc_id": 5958,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Pro2Leu",
"transcript": "NM_006083.4",
"protein_id": "NP_006074.2",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 557,
"cds_start": 5,
"cds_end": null,
"cds_length": 1674,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000417647.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006083.4"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IK",
"gene_hgnc_id": 5958,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Pro2Leu",
"transcript": "ENST00000417647.7",
"protein_id": "ENSP00000396301.2",
"transcript_support_level": 1,
"aa_start": 2,
"aa_end": null,
"aa_length": 557,
"cds_start": 5,
"cds_end": null,
"cds_length": 1674,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006083.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000417647.7"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IK",
"gene_hgnc_id": 5958,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Pro2Leu",
"transcript": "ENST00000947150.1",
"protein_id": "ENSP00000617209.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 497,
"cds_start": 5,
"cds_end": null,
"cds_length": 1494,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947150.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IK",
"gene_hgnc_id": 5958,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Pro2Leu",
"transcript": "ENST00000508301.5",
"protein_id": "ENSP00000422641.1",
"transcript_support_level": 2,
"aa_start": 2,
"aa_end": null,
"aa_length": 266,
"cds_start": 5,
"cds_end": null,
"cds_length": 801,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000508301.5"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IK",
"gene_hgnc_id": 5958,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Pro2Leu",
"transcript": "ENST00000507593.5",
"protein_id": "ENSP00000424622.1",
"transcript_support_level": 3,
"aa_start": 2,
"aa_end": null,
"aa_length": 139,
"cds_start": 5,
"cds_end": null,
"cds_length": 422,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000507593.5"
},
{
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "IK",
"gene_hgnc_id": 5958,
"hgvs_c": "c.5-558C>T",
"hgvs_p": null,
"transcript": "ENST00000513256.5",
"protein_id": "ENSP00000425564.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 106,
"cds_start": null,
"cds_end": null,
"cds_length": 321,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000513256.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IK",
"gene_hgnc_id": 5958,
"hgvs_c": "n.5C>T",
"hgvs_p": null,
"transcript": "ENST00000503332.5",
"protein_id": "ENSP00000421930.1",
"transcript_support_level": 4,
"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": "ENST00000503332.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MIR3655",
"gene_hgnc_id": 38960,
"hgvs_c": "n.70C>T",
"hgvs_p": null,
"transcript": "ENST00000581765.1",
"protein_id": null,
"transcript_support_level": 6,
"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": "miRNA",
"feature": "ENST00000581765.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MIR3655",
"gene_hgnc_id": 38960,
"hgvs_c": "n.70C>T",
"hgvs_p": null,
"transcript": "NR_037428.1",
"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_037428.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IK",
"gene_hgnc_id": 5958,
"hgvs_c": "c.-234C>T",
"hgvs_p": null,
"transcript": "ENST00000502899.2",
"protein_id": "ENSP00000426764.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 211,
"cds_start": null,
"cds_end": null,
"cds_length": 637,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000502899.2"
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMCO6",
"gene_hgnc_id": 28814,
"hgvs_c": "c.*1096C>T",
"hgvs_p": null,
"transcript": "XM_047417354.1",
"protein_id": "XP_047273310.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 400,
"cds_start": null,
"cds_end": null,
"cds_length": 1203,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417354.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFA2",
"gene_hgnc_id": 7685,
"hgvs_c": "n.-142G>A",
"hgvs_p": null,
"transcript": "ENST00000502960.1",
"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": "retained_intron",
"feature": "ENST00000502960.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IK",
"gene_hgnc_id": 5958,
"hgvs_c": "n.-15C>T",
"hgvs_p": null,
"transcript": "ENST00000523672.1",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000523672.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MIR3655",
"gene_hgnc_id": 38960,
"hgvs_c": "n.*49C>T",
"hgvs_p": null,
"transcript": "unassigned_transcript_869",
"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": "miRNA",
"feature": "unassigned_transcript_869"
}
],
"gene_symbol": "IK",
"gene_hgnc_id": 5958,
"dbsnp": "rs1211272992",
"frequency_reference_population": 0.0000013682923,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136829,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4473002851009369,
"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": 0.231,
"revel_prediction": "Benign",
"alphamissense_score": 0.494,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.463,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_006083.4",
"gene_symbol": "IK",
"hgnc_id": 5958,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Pro2Leu"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NR_037428.1",
"gene_symbol": "MIR3655",
"hgnc_id": 38960,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.70C>T",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000502960.1",
"gene_symbol": "NDUFA2",
"hgnc_id": 7685,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.-142G>A",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "XM_047417354.1",
"gene_symbol": "TMCO6",
"hgnc_id": 28814,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*1096C>T",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}