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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: X-133302997-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=133302997&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 133302997,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001448.3",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC4",
"gene_hgnc_id": 4452,
"hgvs_c": "c.1541A>G",
"hgvs_p": "p.Asn514Ser",
"transcript": "NM_001448.3",
"protein_id": "NP_001439.2",
"transcript_support_level": null,
"aa_start": 514,
"aa_end": null,
"aa_length": 556,
"cds_start": 1541,
"cds_end": null,
"cds_length": 1671,
"cdna_start": 2065,
"cdna_end": null,
"cdna_length": 4959,
"mane_select": "ENST00000370828.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001448.3"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC4",
"gene_hgnc_id": 4452,
"hgvs_c": "c.1541A>G",
"hgvs_p": "p.Asn514Ser",
"transcript": "ENST00000370828.4",
"protein_id": "ENSP00000359864.3",
"transcript_support_level": 1,
"aa_start": 514,
"aa_end": null,
"aa_length": 556,
"cds_start": 1541,
"cds_end": null,
"cds_length": 1671,
"cdna_start": 2065,
"cdna_end": null,
"cdna_length": 4959,
"mane_select": "NM_001448.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370828.4"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC4",
"gene_hgnc_id": 4452,
"hgvs_c": "c.1541A>G",
"hgvs_p": "p.Asn514Ser",
"transcript": "ENST00000887818.1",
"protein_id": "ENSP00000557877.1",
"transcript_support_level": null,
"aa_start": 514,
"aa_end": null,
"aa_length": 556,
"cds_start": 1541,
"cds_end": null,
"cds_length": 1671,
"cdna_start": 1679,
"cdna_end": null,
"cdna_length": 3641,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000887818.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC4",
"gene_hgnc_id": 4452,
"hgvs_c": "c.1541A>G",
"hgvs_p": "p.Asn514Ser",
"transcript": "ENST00000931828.1",
"protein_id": "ENSP00000601887.1",
"transcript_support_level": null,
"aa_start": 514,
"aa_end": null,
"aa_length": 556,
"cds_start": 1541,
"cds_end": null,
"cds_length": 1671,
"cdna_start": 1786,
"cdna_end": null,
"cdna_length": 3750,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931828.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC4",
"gene_hgnc_id": 4452,
"hgvs_c": "c.1541A>G",
"hgvs_p": "p.Asn514Ser",
"transcript": "ENST00000931829.1",
"protein_id": "ENSP00000601888.1",
"transcript_support_level": null,
"aa_start": 514,
"aa_end": null,
"aa_length": 556,
"cds_start": 1541,
"cds_end": null,
"cds_length": 1671,
"cdna_start": 1763,
"cdna_end": null,
"cdna_length": 3727,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931829.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC4",
"gene_hgnc_id": 4452,
"hgvs_c": "c.1532A>G",
"hgvs_p": "p.Asn511Ser",
"transcript": "ENST00000931830.1",
"protein_id": "ENSP00000601889.1",
"transcript_support_level": null,
"aa_start": 511,
"aa_end": null,
"aa_length": 553,
"cds_start": 1532,
"cds_end": null,
"cds_length": 1662,
"cdna_start": 2052,
"cdna_end": null,
"cdna_length": 2675,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931830.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC4",
"gene_hgnc_id": 4452,
"hgvs_c": "c.1439A>G",
"hgvs_p": "p.Asn480Ser",
"transcript": "ENST00000887821.1",
"protein_id": "ENSP00000557880.1",
"transcript_support_level": null,
"aa_start": 480,
"aa_end": null,
"aa_length": 522,
"cds_start": 1439,
"cds_end": null,
"cds_length": 1569,
"cdna_start": 1959,
"cdna_end": null,
"cdna_length": 2570,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000887821.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC4",
"gene_hgnc_id": 4452,
"hgvs_c": "c.1394A>G",
"hgvs_p": "p.Asn465Ser",
"transcript": "ENST00000887820.1",
"protein_id": "ENSP00000557879.1",
"transcript_support_level": null,
"aa_start": 465,
"aa_end": null,
"aa_length": 507,
"cds_start": 1394,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 1597,
"cdna_end": null,
"cdna_length": 3558,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000887820.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC4",
"gene_hgnc_id": 4452,
"hgvs_c": "c.1382A>G",
"hgvs_p": "p.Asn461Ser",
"transcript": "ENST00000952996.1",
"protein_id": "ENSP00000623055.1",
"transcript_support_level": null,
"aa_start": 461,
"aa_end": null,
"aa_length": 503,
"cds_start": 1382,
"cds_end": null,
"cds_length": 1512,
"cdna_start": 1906,
"cdna_end": null,
"cdna_length": 2519,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952996.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC4",
"gene_hgnc_id": 4452,
"hgvs_c": "c.1244A>G",
"hgvs_p": "p.Asn415Ser",
"transcript": "ENST00000887819.1",
"protein_id": "ENSP00000557878.1",
"transcript_support_level": null,
"aa_start": 415,
"aa_end": null,
"aa_length": 457,
"cds_start": 1244,
"cds_end": null,
"cds_length": 1374,
"cdna_start": 1470,
"cdna_end": null,
"cdna_length": 3432,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000887819.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPC4",
"gene_hgnc_id": 4452,
"hgvs_c": "c.1097A>G",
"hgvs_p": "p.Asn366Ser",
"transcript": "ENST00000952997.1",
"protein_id": "ENSP00000623056.1",
"transcript_support_level": null,
"aa_start": 366,
"aa_end": null,
"aa_length": 408,
"cds_start": 1097,
"cds_end": null,
"cds_length": 1227,
"cdna_start": 1602,
"cdna_end": null,
"cdna_length": 2207,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952997.1"
}
],
"gene_symbol": "GPC4",
"gene_hgnc_id": 4452,
"dbsnp": "rs927768064",
"frequency_reference_population": 0.000018188388,
"hom_count_reference_population": 8,
"allele_count_reference_population": 22,
"gnomad_exomes_af": 0.0000182129,
"gnomad_genomes_af": 0.0000179464,
"gnomad_exomes_ac": 20,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.08439719676971436,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.131,
"revel_prediction": "Benign",
"alphamissense_score": 0.0634,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.81,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.318,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_001448.3",
"gene_symbol": "GPC4",
"hgnc_id": 4452,
"effects": [
"missense_variant"
],
"inheritance_mode": "XLR,XL",
"hgvs_c": "c.1541A>G",
"hgvs_p": "p.Asn514Ser"
}
],
"clinvar_disease": "Inborn genetic diseases,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Inborn genetic diseases|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}