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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: 13-94577421-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=94577421&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 94577421,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_014305.4",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGDS",
"gene_hgnc_id": 20324,
"hgvs_c": "c.834G>C",
"hgvs_p": "p.Glu278Asp",
"transcript": "NM_014305.4",
"protein_id": "NP_055120.1",
"transcript_support_level": null,
"aa_start": 278,
"aa_end": null,
"aa_length": 350,
"cds_start": 834,
"cds_end": null,
"cds_length": 1053,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000261296.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_014305.4"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGDS",
"gene_hgnc_id": 20324,
"hgvs_c": "c.834G>C",
"hgvs_p": "p.Glu278Asp",
"transcript": "ENST00000261296.7",
"protein_id": "ENSP00000261296.5",
"transcript_support_level": 1,
"aa_start": 278,
"aa_end": null,
"aa_length": 350,
"cds_start": 834,
"cds_end": null,
"cds_length": 1053,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_014305.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000261296.7"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGDS",
"gene_hgnc_id": 20324,
"hgvs_c": "c.804G>C",
"hgvs_p": "p.Glu268Asp",
"transcript": "ENST00000953437.1",
"protein_id": "ENSP00000623496.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 340,
"cds_start": 804,
"cds_end": null,
"cds_length": 1023,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953437.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGDS",
"gene_hgnc_id": 20324,
"hgvs_c": "c.765G>C",
"hgvs_p": "p.Glu255Asp",
"transcript": "ENST00000921421.1",
"protein_id": "ENSP00000591480.1",
"transcript_support_level": null,
"aa_start": 255,
"aa_end": null,
"aa_length": 327,
"cds_start": 765,
"cds_end": null,
"cds_length": 984,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921421.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGDS",
"gene_hgnc_id": 20324,
"hgvs_c": "c.744G>C",
"hgvs_p": "p.Glu248Asp",
"transcript": "ENST00000953436.1",
"protein_id": "ENSP00000623495.1",
"transcript_support_level": null,
"aa_start": 248,
"aa_end": null,
"aa_length": 320,
"cds_start": 744,
"cds_end": null,
"cds_length": 963,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953436.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGDS",
"gene_hgnc_id": 20324,
"hgvs_c": "c.738G>C",
"hgvs_p": "p.Glu246Asp",
"transcript": "NM_001304430.2",
"protein_id": "NP_001291359.1",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 318,
"cds_start": 738,
"cds_end": null,
"cds_length": 957,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001304430.2"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGDS",
"gene_hgnc_id": 20324,
"hgvs_c": "c.501G>C",
"hgvs_p": "p.Glu167Asp",
"transcript": "ENST00000862790.1",
"protein_id": "ENSP00000532849.1",
"transcript_support_level": null,
"aa_start": 167,
"aa_end": null,
"aa_length": 239,
"cds_start": 501,
"cds_end": null,
"cds_length": 720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862790.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGDS",
"gene_hgnc_id": 20324,
"hgvs_c": "c.738G>C",
"hgvs_p": "p.Glu246Asp",
"transcript": "XM_011521065.3",
"protein_id": "XP_011519367.1",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 318,
"cds_start": 738,
"cds_end": null,
"cds_length": 957,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011521065.3"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGDS",
"gene_hgnc_id": 20324,
"hgvs_c": "c.738G>C",
"hgvs_p": "p.Glu246Asp",
"transcript": "XM_011521066.3",
"protein_id": "XP_011519368.1",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 318,
"cds_start": 738,
"cds_end": null,
"cds_length": 957,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011521066.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGDS",
"gene_hgnc_id": 20324,
"hgvs_c": "n.846G>C",
"hgvs_p": null,
"transcript": "NR_130731.2",
"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_130731.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TGDS",
"gene_hgnc_id": 20324,
"hgvs_c": "n.759G>C",
"hgvs_p": null,
"transcript": "NR_130732.2",
"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_130732.2"
}
],
"gene_symbol": "TGDS",
"gene_hgnc_id": 20324,
"dbsnp": "rs546237136",
"frequency_reference_population": 0.00004205777,
"hom_count_reference_population": 0,
"allele_count_reference_population": 66,
"gnomad_exomes_af": 0.0000225825,
"gnomad_genomes_af": 0.000223323,
"gnomad_exomes_ac": 32,
"gnomad_genomes_ac": 34,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.045139968395233154,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.155,
"revel_prediction": "Benign",
"alphamissense_score": 0.0922,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.35,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.316,
"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": "Likely_benign",
"acmg_criteria": "PP2,BP4_Strong",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 4,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_014305.4",
"gene_symbol": "TGDS",
"hgnc_id": 20324,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.834G>C",
"hgvs_p": "p.Glu278Asp"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}