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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: 5-134874466-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=134874466&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 134874466,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_024715.4",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "I",
"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": "TXNDC15",
"gene_hgnc_id": 20652,
"hgvs_c": "c.39G>T",
"hgvs_p": "p.Met13Ile",
"transcript": "NM_024715.4",
"protein_id": "NP_078991.3",
"transcript_support_level": null,
"aa_start": 13,
"aa_end": null,
"aa_length": 360,
"cds_start": 39,
"cds_end": null,
"cds_length": 1083,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000358387.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024715.4"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": true,
"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": "TXNDC15",
"gene_hgnc_id": 20652,
"hgvs_c": "c.39G>T",
"hgvs_p": "p.Met13Ile",
"transcript": "ENST00000358387.9",
"protein_id": "ENSP00000351157.5",
"transcript_support_level": 1,
"aa_start": 13,
"aa_end": null,
"aa_length": 360,
"cds_start": 39,
"cds_end": null,
"cds_length": 1083,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_024715.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000358387.9"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNDC15",
"gene_hgnc_id": 20652,
"hgvs_c": "n.39G>T",
"hgvs_p": null,
"transcript": "ENST00000507024.5",
"protein_id": "ENSP00000424716.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000507024.5"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNDC15",
"gene_hgnc_id": 20652,
"hgvs_c": "n.39G>T",
"hgvs_p": null,
"transcript": "ENST00000511070.5",
"protein_id": "ENSP00000423609.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000511070.5"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNDC15",
"gene_hgnc_id": 20652,
"hgvs_c": "c.39G>T",
"hgvs_p": "p.Met13Ile",
"transcript": "ENST00000926577.1",
"protein_id": "ENSP00000596636.1",
"transcript_support_level": null,
"aa_start": 13,
"aa_end": null,
"aa_length": 372,
"cds_start": 39,
"cds_end": null,
"cds_length": 1119,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926577.1"
},
{
"aa_ref": "M",
"aa_alt": "I",
"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": "TXNDC15",
"gene_hgnc_id": 20652,
"hgvs_c": "c.39G>T",
"hgvs_p": "p.Met13Ile",
"transcript": "ENST00000856994.1",
"protein_id": "ENSP00000527053.1",
"transcript_support_level": null,
"aa_start": 13,
"aa_end": null,
"aa_length": 358,
"cds_start": 39,
"cds_end": null,
"cds_length": 1077,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000856994.1"
},
{
"aa_ref": "M",
"aa_alt": "I",
"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": "TXNDC15",
"gene_hgnc_id": 20652,
"hgvs_c": "c.39G>T",
"hgvs_p": "p.Met13Ile",
"transcript": "ENST00000926578.1",
"protein_id": "ENSP00000596637.1",
"transcript_support_level": null,
"aa_start": 13,
"aa_end": null,
"aa_length": 303,
"cds_start": 39,
"cds_end": null,
"cds_length": 912,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926578.1"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNDC15",
"gene_hgnc_id": 20652,
"hgvs_c": "c.39G>T",
"hgvs_p": "p.Met13Ile",
"transcript": "ENST00000506916.1",
"protein_id": "ENSP00000424220.1",
"transcript_support_level": 3,
"aa_start": 13,
"aa_end": null,
"aa_length": 154,
"cds_start": 39,
"cds_end": null,
"cds_length": 465,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000506916.1"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNDC15",
"gene_hgnc_id": 20652,
"hgvs_c": "c.39G>T",
"hgvs_p": "p.Met13Ile",
"transcript": "ENST00000957250.1",
"protein_id": "ENSP00000627309.1",
"transcript_support_level": null,
"aa_start": 13,
"aa_end": null,
"aa_length": 99,
"cds_start": 39,
"cds_end": null,
"cds_length": 300,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957250.1"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNDC15",
"gene_hgnc_id": 20652,
"hgvs_c": "c.-119G>T",
"hgvs_p": null,
"transcript": "NM_001350735.2",
"protein_id": "NP_001337664.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 292,
"cds_start": null,
"cds_end": null,
"cds_length": 879,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001350735.2"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000300583",
"gene_hgnc_id": null,
"hgvs_c": "n.*202C>A",
"hgvs_p": null,
"transcript": "ENST00000772810.1",
"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": "ENST00000772810.1"
}
],
"gene_symbol": "TXNDC15",
"gene_hgnc_id": 20652,
"dbsnp": "rs373275940",
"frequency_reference_population": 0.000015571319,
"hom_count_reference_population": 0,
"allele_count_reference_population": 25,
"gnomad_exomes_af": 0.0000144503,
"gnomad_genomes_af": 0.0000262702,
"gnomad_exomes_ac": 21,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2810344398021698,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.079,
"revel_prediction": "Benign",
"alphamissense_score": 0.622,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.32,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.002,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_024715.4",
"gene_symbol": "TXNDC15",
"hgnc_id": 20652,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.39G>T",
"hgvs_p": "p.Met13Ile"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000772810.1",
"gene_symbol": "ENSG00000300583",
"hgnc_id": null,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*202C>A",
"hgvs_p": null
}
],
"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
}