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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: 6-7888713-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=7888713&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 7888713,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_030810.5",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNDC5",
"gene_hgnc_id": 21073,
"hgvs_c": "c.955G>T",
"hgvs_p": "p.Ala319Ser",
"transcript": "NM_030810.5",
"protein_id": "NP_110437.2",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 432,
"cds_start": 955,
"cds_end": null,
"cds_length": 1299,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000379757.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_030810.5"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNDC5",
"gene_hgnc_id": 21073,
"hgvs_c": "c.955G>T",
"hgvs_p": "p.Ala319Ser",
"transcript": "ENST00000379757.9",
"protein_id": "ENSP00000369081.4",
"transcript_support_level": 1,
"aa_start": 319,
"aa_end": null,
"aa_length": 432,
"cds_start": 955,
"cds_end": null,
"cds_length": 1299,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_030810.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000379757.9"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNDC5",
"gene_hgnc_id": 21073,
"hgvs_c": "c.631G>T",
"hgvs_p": "p.Ala211Ser",
"transcript": "ENST00000473453.2",
"protein_id": "ENSP00000420784.1",
"transcript_support_level": 1,
"aa_start": 211,
"aa_end": null,
"aa_length": 324,
"cds_start": 631,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000473453.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BLOC1S5-TXNDC5",
"gene_hgnc_id": 42001,
"hgvs_c": "n.*653G>T",
"hgvs_p": null,
"transcript": "ENST00000439343.2",
"protein_id": "ENSP00000454697.1",
"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": "ENST00000439343.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BLOC1S5-TXNDC5",
"gene_hgnc_id": 42001,
"hgvs_c": "n.*653G>T",
"hgvs_p": null,
"transcript": "ENST00000439343.2",
"protein_id": "ENSP00000454697.1",
"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": "ENST00000439343.2"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNDC5",
"gene_hgnc_id": 21073,
"hgvs_c": "c.910G>T",
"hgvs_p": "p.Ala304Ser",
"transcript": "ENST00000933220.1",
"protein_id": "ENSP00000603279.1",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 417,
"cds_start": 910,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933220.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNDC5",
"gene_hgnc_id": 21073,
"hgvs_c": "c.868G>T",
"hgvs_p": "p.Ala290Ser",
"transcript": "ENST00000946227.1",
"protein_id": "ENSP00000616286.1",
"transcript_support_level": null,
"aa_start": 290,
"aa_end": null,
"aa_length": 403,
"cds_start": 868,
"cds_end": null,
"cds_length": 1212,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946227.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNDC5",
"gene_hgnc_id": 21073,
"hgvs_c": "c.631G>T",
"hgvs_p": "p.Ala211Ser",
"transcript": "NM_001145549.4",
"protein_id": "NP_001139021.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 324,
"cds_start": 631,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145549.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "TXNDC5",
"gene_hgnc_id": 21073,
"hgvs_c": "c.819+782G>T",
"hgvs_p": null,
"transcript": "ENST00000933221.1",
"protein_id": "ENSP00000603280.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 384,
"cds_start": null,
"cds_end": null,
"cds_length": 1155,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933221.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "TXNDC5",
"gene_hgnc_id": 21073,
"hgvs_c": "n.733G>T",
"hgvs_p": null,
"transcript": "ENST00000460138.5",
"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": "ENST00000460138.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "TXNDC5",
"gene_hgnc_id": 21073,
"hgvs_c": "n.249G>T",
"hgvs_p": null,
"transcript": "ENST00000475802.1",
"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": "ENST00000475802.1"
},
{
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BLOC1S5-TXNDC5",
"gene_hgnc_id": 42001,
"hgvs_c": "n.1114G>T",
"hgvs_p": null,
"transcript": "NR_037616.1",
"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_037616.1"
}
],
"gene_symbol": "TXNDC5",
"gene_hgnc_id": 21073,
"dbsnp": "rs146368083",
"frequency_reference_population": 0.00003911241,
"hom_count_reference_population": 0,
"allele_count_reference_population": 63,
"gnomad_exomes_af": 0.0000212556,
"gnomad_genomes_af": 0.000210103,
"gnomad_exomes_ac": 31,
"gnomad_genomes_ac": 32,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01626637578010559,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.045,
"revel_prediction": "Benign",
"alphamissense_score": 0.077,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.67,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.958,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_030810.5",
"gene_symbol": "TXNDC5",
"hgnc_id": 21073,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.955G>T",
"hgvs_p": "p.Ala319Ser"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000439343.2",
"gene_symbol": "BLOC1S5-TXNDC5",
"hgnc_id": 42001,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*653G>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
}