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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: 19-1104761-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=1104761&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 5,
"criteria": [
"PM2",
"BP4_Strong",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "GPX4",
"hgnc_id": 4556,
"hgvs_c": "c.27C>G",
"hgvs_p": "p.Pro9Pro",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -3,
"transcript": "NM_001039848.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP7",
"acmg_score": -3,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.85,
"chr": "19",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.8500000238418579,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 197,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 851,
"cdna_start": null,
"cds_end": null,
"cds_length": 594,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_002085.5",
"gene_hgnc_id": 4556,
"gene_symbol": "GPX4",
"hgvs_c": "c.85-425C>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000354171.13",
"protein_coding": true,
"protein_id": "NP_002076.2",
"strand": true,
"transcript": "NM_002085.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 197,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 851,
"cdna_start": null,
"cds_end": null,
"cds_length": 594,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000354171.13",
"gene_hgnc_id": 4556,
"gene_symbol": "GPX4",
"hgvs_c": "c.85-425C>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002085.5",
"protein_coding": true,
"protein_id": "ENSP00000346103.7",
"strand": true,
"transcript": "ENST00000354171.13",
"transcript_support_level": 1
},
{
"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": 793,
"cdna_start": null,
"cds_end": null,
"cds_length": 513,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000611653.4",
"gene_hgnc_id": 4556,
"gene_symbol": "GPX4",
"hgvs_c": "c.4-425C>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000483655.1",
"strand": true,
"transcript": "ENST00000611653.4",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 234,
"aa_ref": "P",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 997,
"cdna_start": 112,
"cds_end": null,
"cds_length": 705,
"cds_start": 27,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001039848.4",
"gene_hgnc_id": 4556,
"gene_symbol": "GPX4",
"hgvs_c": "c.27C>G",
"hgvs_p": "p.Pro9Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001034937.1",
"strand": true,
"transcript": "NM_001039848.4",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 234,
"aa_ref": "P",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 997,
"cdna_start": 112,
"cds_end": null,
"cds_length": 705,
"cds_start": 27,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000585362.7",
"gene_hgnc_id": 4556,
"gene_symbol": "GPX4",
"hgvs_c": "c.27C>G",
"hgvs_p": "p.Pro9Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000473614.3",
"strand": true,
"transcript": "ENST00000585362.7",
"transcript_support_level": 2
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 133,
"aa_ref": "P",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 431,
"cdna_start": 56,
"cds_end": null,
"cds_length": 402,
"cds_start": 27,
"consequences": [
"synonymous_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000614791.1",
"gene_hgnc_id": 4556,
"gene_symbol": "GPX4",
"hgvs_c": "c.27C>G",
"hgvs_p": "p.Pro9Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000484697.1",
"strand": true,
"transcript": "ENST00000614791.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 255,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 826,
"cdna_start": null,
"cds_end": null,
"cds_length": 768,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000593032.6",
"gene_hgnc_id": 4556,
"gene_symbol": "GPX4",
"hgvs_c": "c.4-425C>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000465828.4",
"strand": true,
"transcript": "ENST00000593032.6",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 255,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 826,
"cdna_start": null,
"cds_end": null,
"cds_length": 768,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000706714.1",
"gene_hgnc_id": 4556,
"gene_symbol": "GPX4",
"hgvs_c": "c.4-425C>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000516511.1",
"strand": true,
"transcript": "ENST00000706714.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 242,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 803,
"cdna_start": null,
"cds_end": null,
"cds_length": 729,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000588919.5",
"gene_hgnc_id": 4556,
"gene_symbol": "GPX4",
"hgvs_c": "c.4-425C>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000464989.3",
"strand": true,
"transcript": "ENST00000588919.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 227,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 873,
"cdna_start": null,
"cds_end": null,
"cds_length": 684,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001039847.3",
"gene_hgnc_id": 4556,
"gene_symbol": "GPX4",
"hgvs_c": "c.85-425C>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001034936.1",
"strand": true,
"transcript": "NM_001039847.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 195,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 858,
"cdna_start": null,
"cds_end": null,
"cds_length": 588,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000706713.1",
"gene_hgnc_id": 4556,
"gene_symbol": "GPX4",
"hgvs_c": "c.85-425C>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000516510.1",
"strand": true,
"transcript": "ENST00000706713.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 180,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 812,
"cdna_start": null,
"cds_end": null,
"cds_length": 543,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000589115.6",
"gene_hgnc_id": 4556,
"gene_symbol": "GPX4",
"hgvs_c": "c.85-425C>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000466872.3",
"strand": true,
"transcript": "ENST00000589115.6",
"transcript_support_level": 2
},
{
"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": 788,
"cdna_start": null,
"cds_end": null,
"cds_length": 513,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001367832.1",
"gene_hgnc_id": 4556,
"gene_symbol": "GPX4",
"hgvs_c": "c.4-425C>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001354761.1",
"strand": true,
"transcript": "NM_001367832.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 69,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 824,
"cdna_start": null,
"cds_end": null,
"cds_length": 210,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000706715.1",
"gene_hgnc_id": 4556,
"gene_symbol": "GPX4",
"hgvs_c": "c.-300-425C>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000516512.1",
"strand": true,
"transcript": "ENST00000706715.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1048941130",
"effect": "synonymous_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 4556,
"gene_symbol": "GPX4",
"gnomad_exomes_ac": 0,
"gnomad_exomes_af": 0,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.072,
"pos": 1104761,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001039848.4"
}
]
}