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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: 3-49357420-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=49357420&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 13,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "GPX1",
"hgnc_id": 4553,
"hgvs_c": "c.580G>A",
"hgvs_p": "p.Ala194Thr",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -13,
"transcript": "NM_000581.4",
"verdict": "Benign"
},
{
"benign_score": 13,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"effects": [
"3_prime_UTR_variant"
],
"gene_symbol": "ENSG00000290318",
"hgnc_id": null,
"hgvs_c": "c.*300G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -13,
"transcript": "ENST00000704381.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_score": -13,
"allele_count_reference_population": 4042,
"alphamissense_prediction": null,
"alphamissense_score": 0.0878,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.68,
"chr": "3",
"clinvar_classification": "Benign",
"clinvar_disease": "GPX1-related disorder",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.005723923444747925,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 203,
"aa_ref": "A",
"aa_start": 194,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 899,
"cdna_start": 655,
"cds_end": null,
"cds_length": 612,
"cds_start": 580,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_000581.4",
"gene_hgnc_id": 4553,
"gene_symbol": "GPX1",
"hgvs_c": "c.580G>A",
"hgvs_p": "p.Ala194Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000419783.3",
"protein_coding": true,
"protein_id": "NP_000572.2",
"strand": false,
"transcript": "NM_000581.4",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 203,
"aa_ref": "A",
"aa_start": 194,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 899,
"cdna_start": 655,
"cds_end": null,
"cds_length": 612,
"cds_start": 580,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000419783.3",
"gene_hgnc_id": 4553,
"gene_symbol": "GPX1",
"hgvs_c": "c.580G>A",
"hgvs_p": "p.Ala194Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000581.4",
"protein_coding": true,
"protein_id": "ENSP00000407375.1",
"strand": false,
"transcript": "ENST00000419783.3",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 163,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1270,
"cdna_start": null,
"cds_end": null,
"cds_length": 492,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000704381.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000290318",
"hgvs_c": "c.*300G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515884.1",
"strand": false,
"transcript": "ENST00000704381.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 202,
"aa_ref": "A",
"aa_start": 193,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1150,
"cdna_start": 904,
"cds_end": null,
"cds_length": 609,
"cds_start": 577,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000703795.1",
"gene_hgnc_id": 4553,
"gene_symbol": "GPX1",
"hgvs_c": "c.577G>A",
"hgvs_p": "p.Ala193Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515480.1",
"strand": false,
"transcript": "ENST00000703795.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 190,
"aa_ref": "A",
"aa_start": 181,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 791,
"cdna_start": 547,
"cds_end": null,
"cds_length": 573,
"cds_start": 541,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000703796.1",
"gene_hgnc_id": 4553,
"gene_symbol": "GPX1",
"hgvs_c": "c.541G>A",
"hgvs_p": "p.Ala181Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515481.1",
"strand": false,
"transcript": "ENST00000703796.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 157,
"aa_ref": "A",
"aa_start": 148,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 761,
"cdna_start": 517,
"cds_end": null,
"cds_length": 474,
"cds_start": 442,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001329455.2",
"gene_hgnc_id": 4553,
"gene_symbol": "GPX1",
"hgvs_c": "c.442G>A",
"hgvs_p": "p.Ala148Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001316384.1",
"strand": false,
"transcript": "NM_001329455.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 157,
"aa_ref": "A",
"aa_start": 148,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 761,
"cdna_start": 517,
"cds_end": null,
"cds_length": 474,
"cds_start": 442,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000643797.2",
"gene_hgnc_id": 4553,
"gene_symbol": "GPX1",
"hgvs_c": "c.442G>A",
"hgvs_p": "p.Ala148Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000495108.1",
"strand": false,
"transcript": "ENST00000643797.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 148,
"aa_ref": "A",
"aa_start": 139,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 703,
"cdna_start": 459,
"cds_end": null,
"cds_length": 447,
"cds_start": 415,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000704374.1",
"gene_hgnc_id": 4553,
"gene_symbol": "GPX1",
"hgvs_c": "c.415G>A",
"hgvs_p": "p.Ala139Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515879.1",
"strand": false,
"transcript": "ENST00000704374.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 122,
"aa_ref": "A",
"aa_start": 113,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 625,
"cdna_start": 384,
"cds_end": null,
"cds_length": 369,
"cds_start": 337,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000704356.1",
"gene_hgnc_id": 4553,
"gene_symbol": "GPX1",
"hgvs_c": "c.337G>A",
"hgvs_p": "p.Ala113Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515867.1",
"strand": false,
"transcript": "ENST00000704356.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 170,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 918,
"cdna_start": null,
"cds_end": null,
"cds_length": 513,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001329503.2",
"gene_hgnc_id": 4553,
"gene_symbol": "GPX1",
"hgvs_c": "c.*86G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001316432.1",
"strand": false,
"transcript": "NM_001329503.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 170,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 942,
"cdna_start": null,
"cds_end": null,
"cds_length": 513,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000646881.3",
"gene_hgnc_id": 4553,
"gene_symbol": "GPX1",
"hgvs_c": "c.*86G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000495001.2",
"strand": false,
"transcript": "ENST00000646881.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 124,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 683,
"cdna_start": null,
"cds_end": null,
"cds_length": 375,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000704378.1",
"gene_hgnc_id": 4553,
"gene_symbol": "GPX1",
"hgvs_c": "c.*20G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515883.1",
"strand": false,
"transcript": "ENST00000704378.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 104,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1040,
"cdna_start": null,
"cds_end": null,
"cds_length": 315,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001329502.2",
"gene_hgnc_id": 4553,
"gene_symbol": "GPX1",
"hgvs_c": "c.*406G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001316431.1",
"strand": false,
"transcript": "NM_001329502.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 104,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1012,
"cdna_start": null,
"cds_end": null,
"cds_length": 315,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000496791.3",
"gene_hgnc_id": 4553,
"gene_symbol": "GPX1",
"hgvs_c": "c.*406G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000493593.2",
"strand": false,
"transcript": "ENST00000496791.3",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 98,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1178,
"cdna_start": null,
"cds_end": null,
"cds_length": 297,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_201397.3",
"gene_hgnc_id": 4553,
"gene_symbol": "GPX1",
"hgvs_c": "c.*562G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_958799.1",
"strand": false,
"transcript": "NM_201397.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 98,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1148,
"cdna_start": null,
"cds_end": null,
"cds_length": 297,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000419349.3",
"gene_hgnc_id": 4553,
"gene_symbol": "GPX1",
"hgvs_c": "c.*562G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000391316.1",
"strand": false,
"transcript": "ENST00000419349.3",
"transcript_support_level": 6
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 98,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 970,
"cdna_start": null,
"cds_end": null,
"cds_length": 297,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000704375.1",
"gene_hgnc_id": 4553,
"gene_symbol": "GPX1",
"hgvs_c": "c.*354G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515880.1",
"strand": false,
"transcript": "ENST00000704375.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 51,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 462,
"cdna_start": null,
"cds_end": null,
"cds_length": 156,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000704376.1",
"gene_hgnc_id": 4553,
"gene_symbol": "GPX1",
"hgvs_c": "c.*20G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515881.1",
"strand": false,
"transcript": "ENST00000704376.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 46,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 449,
"cdna_start": null,
"cds_end": null,
"cds_length": 141,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000704377.1",
"gene_hgnc_id": 4553,
"gene_symbol": "GPX1",
"hgvs_c": "c.*20G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515882.1",
"strand": false,
"transcript": "ENST00000704377.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1080,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000703797.1",
"gene_hgnc_id": 4553,
"gene_symbol": "GPX1",
"hgvs_c": "n.*473G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000515482.1",
"strand": false,
"transcript": "ENST00000703797.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 697,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000704379.1",
"gene_hgnc_id": null,
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