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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: 17-50110054-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=50110054&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 50110054,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_002611.5",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDK2",
"gene_hgnc_id": 8810,
"hgvs_c": "c.1181C>A",
"hgvs_p": "p.Pro394His",
"transcript": "NM_002611.5",
"protein_id": "NP_002602.2",
"transcript_support_level": null,
"aa_start": 394,
"aa_end": null,
"aa_length": 407,
"cds_start": 1181,
"cds_end": null,
"cds_length": 1224,
"cdna_start": 1266,
"cdna_end": null,
"cdna_length": 3364,
"mane_select": "ENST00000503176.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDK2",
"gene_hgnc_id": 8810,
"hgvs_c": "c.1181C>A",
"hgvs_p": "p.Pro394His",
"transcript": "ENST00000503176.6",
"protein_id": "ENSP00000420927.1",
"transcript_support_level": 1,
"aa_start": 394,
"aa_end": null,
"aa_length": 407,
"cds_start": 1181,
"cds_end": null,
"cds_length": 1224,
"cdna_start": 1266,
"cdna_end": null,
"cdna_length": 3364,
"mane_select": "NM_002611.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAMD14",
"gene_hgnc_id": 27312,
"hgvs_c": "c.*2839G>T",
"hgvs_p": null,
"transcript": "NM_001257359.2",
"protein_id": "NP_001244288.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 417,
"cds_start": -4,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4763,
"mane_select": "ENST00000330175.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAMD14",
"gene_hgnc_id": 27312,
"hgvs_c": "c.*2839G>T",
"hgvs_p": null,
"transcript": "ENST00000330175.9",
"protein_id": "ENSP00000329144.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 417,
"cds_start": -4,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4763,
"mane_select": "NM_001257359.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDK2",
"gene_hgnc_id": 8810,
"hgvs_c": "c.989C>A",
"hgvs_p": "p.Pro330His",
"transcript": "NM_001199898.2",
"protein_id": "NP_001186827.1",
"transcript_support_level": null,
"aa_start": 330,
"aa_end": null,
"aa_length": 343,
"cds_start": 989,
"cds_end": null,
"cds_length": 1032,
"cdna_start": 1380,
"cdna_end": null,
"cdna_length": 3478,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDK2",
"gene_hgnc_id": 8810,
"hgvs_c": "c.989C>A",
"hgvs_p": "p.Pro330His",
"transcript": "NM_001199899.2",
"protein_id": "NP_001186828.1",
"transcript_support_level": null,
"aa_start": 330,
"aa_end": null,
"aa_length": 343,
"cds_start": 989,
"cds_end": null,
"cds_length": 1032,
"cdna_start": 1179,
"cdna_end": null,
"cdna_length": 3277,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDK2",
"gene_hgnc_id": 8810,
"hgvs_c": "c.989C>A",
"hgvs_p": "p.Pro330His",
"transcript": "ENST00000007708.7",
"protein_id": "ENSP00000007708.3",
"transcript_support_level": 2,
"aa_start": 330,
"aa_end": null,
"aa_length": 343,
"cds_start": 989,
"cds_end": null,
"cds_length": 1032,
"cdna_start": 1380,
"cdna_end": null,
"cdna_length": 2384,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDK2",
"gene_hgnc_id": 8810,
"hgvs_c": "c.989C>A",
"hgvs_p": "p.Pro330His",
"transcript": "ENST00000614357.4",
"protein_id": "ENSP00000481915.1",
"transcript_support_level": 5,
"aa_start": 330,
"aa_end": null,
"aa_length": 343,
"cds_start": 989,
"cds_end": null,
"cds_length": 1032,
"cdna_start": 1179,
"cdna_end": null,
"cdna_length": 2493,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDK2",
"gene_hgnc_id": 8810,
"hgvs_c": "n.651C>A",
"hgvs_p": null,
"transcript": "ENST00000512204.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 806,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAMD14",
"gene_hgnc_id": 27312,
"hgvs_c": "c.*2839G>T",
"hgvs_p": null,
"transcript": "NM_174920.4",
"protein_id": "NP_777580.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 445,
"cds_start": -4,
"cds_end": null,
"cds_length": 1338,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4847,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAMD14",
"gene_hgnc_id": 27312,
"hgvs_c": "c.*2839G>T",
"hgvs_p": null,
"transcript": "XM_017024322.3",
"protein_id": "XP_016879811.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 500,
"cds_start": -4,
"cds_end": null,
"cds_length": 1503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4371,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDK2",
"gene_hgnc_id": 8810,
"hgvs_c": "n.*70C>A",
"hgvs_p": null,
"transcript": "ENST00000506647.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 660,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PDK2",
"gene_hgnc_id": 8810,
"dbsnp": null,
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7726556062698364,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.396,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8224,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.1,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.87,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.01,
"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_002611.5",
"gene_symbol": "PDK2",
"hgnc_id": 8810,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1181C>A",
"hgvs_p": "p.Pro394His"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001257359.2",
"gene_symbol": "SAMD14",
"hgnc_id": 27312,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*2839G>T",
"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
}