← Back to variant description
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: 19-12800211-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=12800211&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 12800211,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_005809.6",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDX2",
"gene_hgnc_id": 9353,
"hgvs_c": "c.346G>A",
"hgvs_p": "p.Gly116Ser",
"transcript": "NM_005809.6",
"protein_id": "NP_005800.3",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 198,
"cds_start": 346,
"cds_end": null,
"cds_length": 597,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000301522.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005809.6"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDX2",
"gene_hgnc_id": 9353,
"hgvs_c": "c.346G>A",
"hgvs_p": "p.Gly116Ser",
"transcript": "ENST00000301522.3",
"protein_id": "ENSP00000301522.2",
"transcript_support_level": 1,
"aa_start": 116,
"aa_end": null,
"aa_length": 198,
"cds_start": 346,
"cds_end": null,
"cds_length": 597,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005809.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000301522.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDX2",
"gene_hgnc_id": 9353,
"hgvs_c": "n.1021G>A",
"hgvs_p": null,
"transcript": "ENST00000466174.5",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000466174.5"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDX2",
"gene_hgnc_id": 9353,
"hgvs_c": "c.346G>A",
"hgvs_p": "p.Gly116Ser",
"transcript": "ENST00000866180.1",
"protein_id": "ENSP00000536239.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 212,
"cds_start": 346,
"cds_end": null,
"cds_length": 639,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866180.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDX2",
"gene_hgnc_id": 9353,
"hgvs_c": "c.346G>A",
"hgvs_p": "p.Gly116Ser",
"transcript": "ENST00000866178.1",
"protein_id": "ENSP00000536237.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 198,
"cds_start": 346,
"cds_end": null,
"cds_length": 597,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866178.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDX2",
"gene_hgnc_id": 9353,
"hgvs_c": "c.346G>A",
"hgvs_p": "p.Gly116Ser",
"transcript": "ENST00000866181.1",
"protein_id": "ENSP00000536240.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 198,
"cds_start": 346,
"cds_end": null,
"cds_length": 597,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866181.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDX2",
"gene_hgnc_id": 9353,
"hgvs_c": "c.346G>A",
"hgvs_p": "p.Gly116Ser",
"transcript": "ENST00000955165.1",
"protein_id": "ENSP00000625224.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 198,
"cds_start": 346,
"cds_end": null,
"cds_length": 597,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955165.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDX2",
"gene_hgnc_id": 9353,
"hgvs_c": "c.346G>A",
"hgvs_p": "p.Gly116Ser",
"transcript": "ENST00000334482.9",
"protein_id": "ENSP00000334063.5",
"transcript_support_level": 3,
"aa_start": 116,
"aa_end": null,
"aa_length": 136,
"cds_start": 346,
"cds_end": null,
"cds_length": 411,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000334482.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDX2",
"gene_hgnc_id": 9353,
"hgvs_c": "n.404G>A",
"hgvs_p": null,
"transcript": "ENST00000477555.1",
"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": "ENST00000477555.1"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDX2",
"gene_hgnc_id": 9353,
"hgvs_c": "n.251G>A",
"hgvs_p": null,
"transcript": "ENST00000478908.1",
"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": "ENST00000478908.1"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDX2",
"gene_hgnc_id": 9353,
"hgvs_c": "n.37G>A",
"hgvs_p": null,
"transcript": "ENST00000498785.1",
"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": "ENST00000498785.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000267062",
"gene_hgnc_id": null,
"hgvs_c": "n.201-1543C>T",
"hgvs_p": null,
"transcript": "ENST00000585496.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000585496.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "HOOK2",
"gene_hgnc_id": 19885,
"hgvs_c": "n.41+24967G>A",
"hgvs_p": null,
"transcript": "ENST00000589765.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000589765.1"
}
],
"gene_symbol": "PRDX2",
"gene_hgnc_id": 9353,
"dbsnp": "rs566102951",
"frequency_reference_population": 0.000077458564,
"hom_count_reference_population": 0,
"allele_count_reference_population": 125,
"gnomad_exomes_af": 0.0000759417,
"gnomad_genomes_af": 0.0000920338,
"gnomad_exomes_ac": 111,
"gnomad_genomes_ac": 14,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.813608705997467,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.35,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.4103,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.23,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.546,
"phylop100way_prediction": "Pathogenic",
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3,BS2",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 4,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_005809.6",
"gene_symbol": "PRDX2",
"hgnc_id": 9353,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.346G>A",
"hgvs_p": "p.Gly116Ser"
},
{
"score": 1,
"benign_score": 0,
"pathogenic_score": 1,
"criteria": [
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000585496.1",
"gene_symbol": "ENSG00000267062",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.201-1543C>T",
"hgvs_p": null
},
{
"score": 1,
"benign_score": 0,
"pathogenic_score": 1,
"criteria": [
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000589765.1",
"gene_symbol": "HOOK2",
"hgnc_id": 19885,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.41+24967G>A",
"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
}