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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: 16-286916-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=286916&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PDIA2",
"hgnc_id": 14180,
"hgvs_c": "c.1504C>T",
"hgvs_p": "p.Pro502Ser",
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -12,
"transcript": "NM_006849.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_score": -12,
"allele_count_reference_population": 250605,
"alphamissense_prediction": null,
"alphamissense_score": 0.0733,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.68,
"chr": "16",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.00202256441116333,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 525,
"aa_ref": "P",
"aa_start": 502,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1686,
"cdna_start": 1510,
"cds_end": null,
"cds_length": 1578,
"cds_start": 1504,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_006849.4",
"gene_hgnc_id": 14180,
"gene_symbol": "PDIA2",
"hgvs_c": "c.1504C>T",
"hgvs_p": "p.Pro502Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000219406.11",
"protein_coding": true,
"protein_id": "NP_006840.2",
"strand": true,
"transcript": "NM_006849.4",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 525,
"aa_ref": "P",
"aa_start": 502,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1686,
"cdna_start": 1510,
"cds_end": null,
"cds_length": 1578,
"cds_start": 1504,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000219406.11",
"gene_hgnc_id": 14180,
"gene_symbol": "PDIA2",
"hgvs_c": "c.1504C>T",
"hgvs_p": "p.Pro502Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006849.4",
"protein_coding": true,
"protein_id": "ENSP00000219406.7",
"strand": true,
"transcript": "ENST00000219406.11",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1956,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000482665.1",
"gene_hgnc_id": 14180,
"gene_symbol": "PDIA2",
"hgvs_c": "n.1787C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000482665.1",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 522,
"aa_ref": "P",
"aa_start": 499,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1575,
"cdna_start": 1500,
"cds_end": null,
"cds_length": 1569,
"cds_start": 1495,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000404312.5",
"gene_hgnc_id": 14180,
"gene_symbol": "PDIA2",
"hgvs_c": "c.1495C>T",
"hgvs_p": "p.Pro499Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000384410.1",
"strand": true,
"transcript": "ENST00000404312.5",
"transcript_support_level": 5
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 493,
"aa_ref": "P",
"aa_start": 470,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1601,
"cdna_start": 1426,
"cds_end": null,
"cds_length": 1482,
"cds_start": 1408,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000964532.1",
"gene_hgnc_id": 14180,
"gene_symbol": "PDIA2",
"hgvs_c": "c.1408C>T",
"hgvs_p": "p.Pro470Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000634591.1",
"strand": true,
"transcript": "ENST00000964532.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 483,
"aa_ref": "P",
"aa_start": 460,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1559,
"cdna_start": 1384,
"cds_end": null,
"cds_length": 1452,
"cds_start": 1378,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000964534.1",
"gene_hgnc_id": 14180,
"gene_symbol": "PDIA2",
"hgvs_c": "c.1378C>T",
"hgvs_p": "p.Pro460Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000634593.1",
"strand": true,
"transcript": "ENST00000964534.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 444,
"aa_ref": "P",
"aa_start": 421,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1455,
"cdna_start": 1279,
"cds_end": null,
"cds_length": 1335,
"cds_start": 1261,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000851624.1",
"gene_hgnc_id": 14180,
"gene_symbol": "PDIA2",
"hgvs_c": "c.1261C>T",
"hgvs_p": "p.Pro421Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000521683.1",
"strand": true,
"transcript": "ENST00000851624.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 429,
"aa_ref": "P",
"aa_start": 406,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1401,
"cdna_start": 1226,
"cds_end": null,
"cds_length": 1290,
"cds_start": 1216,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000964533.1",
"gene_hgnc_id": 14180,
"gene_symbol": "PDIA2",
"hgvs_c": "c.1216C>T",
"hgvs_p": "p.Pro406Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000634592.1",
"strand": true,
"transcript": "ENST00000964533.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 154,
"aa_ref": "P",
"aa_start": 131,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 567,
"cdna_start": 391,
"cds_end": null,
"cds_length": 465,
"cds_start": 391,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000435833.1",
"gene_hgnc_id": 14180,
"gene_symbol": "PDIA2",
"hgvs_c": "c.391C>T",
"hgvs_p": "p.Pro131Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000405081.1",
"strand": true,
"transcript": "ENST00000435833.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 488,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1569,
"cdna_start": null,
"cds_end": null,
"cds_length": 1467,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 10,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000964535.1",
"gene_hgnc_id": 14180,
"gene_symbol": "PDIA2",
"hgvs_c": "c.1423-153C>T",
"hgvs_p": null,
"intron_rank": 9,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000634594.1",
"strand": true,
"transcript": "ENST00000964535.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1750,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000467212.5",
"gene_hgnc_id": 14180,
"gene_symbol": "PDIA2",
"hgvs_c": "n.1575C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000467212.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1048786",
"effect": "missense_variant",
"frequency_reference_population": 0.15686755,
"gene_hgnc_id": 14180,
"gene_symbol": "PDIA2",
"gnomad_exomes_ac": 230676,
"gnomad_exomes_af": 0.159605,
"gnomad_exomes_homalt": 18851,
"gnomad_genomes_ac": 19929,
"gnomad_genomes_af": 0.130885,
"gnomad_genomes_homalt": 1481,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 20332,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.462,
"pos": 286916,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.015,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_006849.4"
}
]
}