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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: 12-103980016-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=103980016&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 103980016,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_003211.6",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TDG",
"gene_hgnc_id": 11700,
"hgvs_c": "c.352G>A",
"hgvs_p": "p.Glu118Lys",
"transcript": "NM_003211.6",
"protein_id": "NP_003202.3",
"transcript_support_level": null,
"aa_start": 118,
"aa_end": null,
"aa_length": 410,
"cds_start": 352,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000392872.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003211.6"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TDG",
"gene_hgnc_id": 11700,
"hgvs_c": "c.352G>A",
"hgvs_p": "p.Glu118Lys",
"transcript": "ENST00000392872.8",
"protein_id": "ENSP00000376611.3",
"transcript_support_level": 1,
"aa_start": 118,
"aa_end": null,
"aa_length": 410,
"cds_start": 352,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003211.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000392872.8"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TDG",
"gene_hgnc_id": 11700,
"hgvs_c": "c.340G>A",
"hgvs_p": "p.Glu114Lys",
"transcript": "ENST00000266775.13",
"protein_id": "ENSP00000266775.9",
"transcript_support_level": 1,
"aa_start": 114,
"aa_end": null,
"aa_length": 406,
"cds_start": 340,
"cds_end": null,
"cds_length": 1221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000266775.13"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TDG",
"gene_hgnc_id": 11700,
"hgvs_c": "n.487G>A",
"hgvs_p": null,
"transcript": "ENST00000544060.1",
"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": "retained_intron",
"feature": "ENST00000544060.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TDG",
"gene_hgnc_id": 11700,
"hgvs_c": "n.405G>A",
"hgvs_p": null,
"transcript": "ENST00000545698.1",
"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": "retained_intron",
"feature": "ENST00000545698.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TDG",
"gene_hgnc_id": 11700,
"hgvs_c": "c.352G>A",
"hgvs_p": "p.Glu118Lys",
"transcript": "ENST00000537100.5",
"protein_id": "ENSP00000439825.1",
"transcript_support_level": 3,
"aa_start": 118,
"aa_end": null,
"aa_length": 256,
"cds_start": 352,
"cds_end": null,
"cds_length": 771,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000537100.5"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TDG",
"gene_hgnc_id": 11700,
"hgvs_c": "c.277G>A",
"hgvs_p": "p.Glu93Lys",
"transcript": "ENST00000436021.6",
"protein_id": "ENSP00000390167.2",
"transcript_support_level": 5,
"aa_start": 93,
"aa_end": null,
"aa_length": 137,
"cds_start": 277,
"cds_end": null,
"cds_length": 415,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000436021.6"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TDG",
"gene_hgnc_id": 11700,
"hgvs_c": "c.340G>A",
"hgvs_p": "p.Glu114Lys",
"transcript": "XM_047429486.1",
"protein_id": "XP_047285442.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 406,
"cds_start": 340,
"cds_end": null,
"cds_length": 1221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047429486.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TDG",
"gene_hgnc_id": 11700,
"hgvs_c": "c.-78G>A",
"hgvs_p": null,
"transcript": "NM_001363612.2",
"protein_id": "NP_001350541.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 267,
"cds_start": null,
"cds_end": null,
"cds_length": 804,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001363612.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TDG",
"gene_hgnc_id": 11700,
"hgvs_c": "c.-78G>A",
"hgvs_p": null,
"transcript": "ENST00000544861.5",
"protein_id": "ENSP00000445899.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 267,
"cds_start": null,
"cds_end": null,
"cds_length": 804,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000544861.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TDG",
"gene_hgnc_id": 11700,
"hgvs_c": "c.-228G>A",
"hgvs_p": null,
"transcript": "XM_047429488.1",
"protein_id": "XP_047285444.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 267,
"cds_start": null,
"cds_end": null,
"cds_length": 804,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047429488.1"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TDG",
"gene_hgnc_id": 11700,
"hgvs_c": "n.61G>A",
"hgvs_p": null,
"transcript": "ENST00000540956.1",
"protein_id": "ENSP00000445716.1",
"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": "ENST00000540956.1"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TDG",
"gene_hgnc_id": 11700,
"hgvs_c": "n.152G>A",
"hgvs_p": null,
"transcript": "ENST00000542926.5",
"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": "retained_intron",
"feature": "ENST00000542926.5"
},
{
"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": "TDG",
"gene_hgnc_id": 11700,
"hgvs_c": "c.-633G>A",
"hgvs_p": null,
"transcript": "XM_047429487.1",
"protein_id": "XP_047285443.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 267,
"cds_start": null,
"cds_end": null,
"cds_length": 804,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047429487.1"
}
],
"gene_symbol": "TDG",
"gene_hgnc_id": 11700,
"dbsnp": "rs763015383",
"frequency_reference_population": 0.0000020525677,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205257,
"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": 0.7392817735671997,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.574,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8364,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.19,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.652,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.04,
"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_003211.6",
"gene_symbol": "TDG",
"hgnc_id": 11700,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.352G>A",
"hgvs_p": "p.Glu118Lys"
}
],
"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
}