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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: 3-53178479-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=53178479&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 53178479,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_006254.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCD",
"gene_hgnc_id": 9399,
"hgvs_c": "c.57C>T",
"hgvs_p": "p.Ala19Ala",
"transcript": "NM_006254.4",
"protein_id": "NP_006245.2",
"transcript_support_level": null,
"aa_start": 19,
"aa_end": null,
"aa_length": 676,
"cds_start": 57,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 408,
"cdna_end": null,
"cdna_length": 2833,
"mane_select": "ENST00000330452.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCD",
"gene_hgnc_id": 9399,
"hgvs_c": "c.57C>T",
"hgvs_p": "p.Ala19Ala",
"transcript": "ENST00000330452.8",
"protein_id": "ENSP00000331602.3",
"transcript_support_level": 1,
"aa_start": 19,
"aa_end": null,
"aa_length": 676,
"cds_start": 57,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 408,
"cdna_end": null,
"cdna_length": 2833,
"mane_select": "NM_006254.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCD",
"gene_hgnc_id": 9399,
"hgvs_c": "c.57C>T",
"hgvs_p": "p.Ala19Ala",
"transcript": "ENST00000394729.6",
"protein_id": "ENSP00000378217.2",
"transcript_support_level": 1,
"aa_start": 19,
"aa_end": null,
"aa_length": 676,
"cds_start": 57,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 385,
"cdna_end": null,
"cdna_length": 2810,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCD",
"gene_hgnc_id": 9399,
"hgvs_c": "c.114C>T",
"hgvs_p": "p.Ala38Ala",
"transcript": "NM_001354676.2",
"protein_id": "NP_001341605.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 695,
"cds_start": 114,
"cds_end": null,
"cds_length": 2088,
"cdna_start": 194,
"cdna_end": null,
"cdna_length": 2619,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCD",
"gene_hgnc_id": 9399,
"hgvs_c": "c.105C>T",
"hgvs_p": "p.Ala35Ala",
"transcript": "NM_001354678.2",
"protein_id": "NP_001341607.1",
"transcript_support_level": null,
"aa_start": 35,
"aa_end": null,
"aa_length": 692,
"cds_start": 105,
"cds_end": null,
"cds_length": 2079,
"cdna_start": 185,
"cdna_end": null,
"cdna_length": 2610,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCD",
"gene_hgnc_id": 9399,
"hgvs_c": "c.57C>T",
"hgvs_p": "p.Ala19Ala",
"transcript": "NM_001316327.2",
"protein_id": "NP_001303256.1",
"transcript_support_level": null,
"aa_start": 19,
"aa_end": null,
"aa_length": 676,
"cds_start": 57,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 257,
"cdna_end": null,
"cdna_length": 2682,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCD",
"gene_hgnc_id": 9399,
"hgvs_c": "c.57C>T",
"hgvs_p": "p.Ala19Ala",
"transcript": "NM_001354679.2",
"protein_id": "NP_001341608.1",
"transcript_support_level": null,
"aa_start": 19,
"aa_end": null,
"aa_length": 676,
"cds_start": 57,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 412,
"cdna_end": null,
"cdna_length": 2837,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCD",
"gene_hgnc_id": 9399,
"hgvs_c": "c.57C>T",
"hgvs_p": "p.Ala19Ala",
"transcript": "NM_001354680.2",
"protein_id": "NP_001341609.1",
"transcript_support_level": null,
"aa_start": 19,
"aa_end": null,
"aa_length": 676,
"cds_start": 57,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 524,
"cdna_end": null,
"cdna_length": 2949,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCD",
"gene_hgnc_id": 9399,
"hgvs_c": "c.57C>T",
"hgvs_p": "p.Ala19Ala",
"transcript": "NM_212539.2",
"protein_id": "NP_997704.1",
"transcript_support_level": null,
"aa_start": 19,
"aa_end": null,
"aa_length": 676,
"cds_start": 57,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 296,
"cdna_end": null,
"cdna_length": 2721,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCD",
"gene_hgnc_id": 9399,
"hgvs_c": "c.57C>T",
"hgvs_p": "p.Ala19Ala",
"transcript": "ENST00000650739.1",
"protein_id": "ENSP00000498623.1",
"transcript_support_level": null,
"aa_start": 19,
"aa_end": null,
"aa_length": 676,
"cds_start": 57,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 265,
"cdna_end": null,
"cdna_length": 2531,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCD",
"gene_hgnc_id": 9399,
"hgvs_c": "c.57C>T",
"hgvs_p": "p.Ala19Ala",
"transcript": "ENST00000652449.1",
"protein_id": "ENSP00000498400.1",
"transcript_support_level": null,
"aa_start": 19,
"aa_end": null,
"aa_length": 676,
"cds_start": 57,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 516,
"cdna_end": null,
"cdna_length": 2711,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCD",
"gene_hgnc_id": 9399,
"hgvs_c": "c.57C>T",
"hgvs_p": "p.Ala19Ala",
"transcript": "ENST00000654719.1",
"protein_id": "ENSP00000499558.1",
"transcript_support_level": null,
"aa_start": 19,
"aa_end": null,
"aa_length": 676,
"cds_start": 57,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 100,
"cdna_end": null,
"cdna_length": 2262,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCD",
"gene_hgnc_id": 9399,
"hgvs_c": "c.57C>T",
"hgvs_p": "p.Ala19Ala",
"transcript": "ENST00000650940.1",
"protein_id": "ENSP00000499184.1",
"transcript_support_level": null,
"aa_start": 19,
"aa_end": null,
"aa_length": 294,
"cds_start": 57,
"cds_end": null,
"cds_length": 885,
"cdna_start": 147,
"cdna_end": null,
"cdna_length": 975,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCD",
"gene_hgnc_id": 9399,
"hgvs_c": "c.57C>T",
"hgvs_p": "p.Ala19Ala",
"transcript": "ENST00000464818.1",
"protein_id": "ENSP00000419629.1",
"transcript_support_level": 5,
"aa_start": 19,
"aa_end": null,
"aa_length": 222,
"cds_start": 57,
"cds_end": null,
"cds_length": 671,
"cdna_start": 163,
"cdna_end": null,
"cdna_length": 777,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCD",
"gene_hgnc_id": 9399,
"hgvs_c": "c.57C>T",
"hgvs_p": "p.Ala19Ala",
"transcript": "ENST00000487897.5",
"protein_id": "ENSP00000418106.1",
"transcript_support_level": 4,
"aa_start": 19,
"aa_end": null,
"aa_length": 124,
"cds_start": 57,
"cds_end": null,
"cds_length": 376,
"cdna_start": 243,
"cdna_end": null,
"cdna_length": 562,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCD",
"gene_hgnc_id": 9399,
"hgvs_c": "c.57C>T",
"hgvs_p": "p.Ala19Ala",
"transcript": "ENST00000478843.5",
"protein_id": "ENSP00000419726.1",
"transcript_support_level": 4,
"aa_start": 19,
"aa_end": null,
"aa_length": 76,
"cds_start": 57,
"cds_end": null,
"cds_length": 233,
"cdna_start": 413,
"cdna_end": null,
"cdna_length": 589,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCD",
"gene_hgnc_id": 9399,
"hgvs_c": "c.57C>T",
"hgvs_p": "p.Ala19Ala",
"transcript": "ENST00000477794.2",
"protein_id": "ENSP00000498857.1",
"transcript_support_level": 3,
"aa_start": 19,
"aa_end": null,
"aa_length": 37,
"cds_start": 57,
"cds_end": null,
"cds_length": 115,
"cdna_start": 346,
"cdna_end": null,
"cdna_length": 404,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCD",
"gene_hgnc_id": 9399,
"hgvs_c": "c.57C>T",
"hgvs_p": "p.Ala19Ala",
"transcript": "XM_047448564.1",
"protein_id": "XP_047304520.1",
"transcript_support_level": null,
"aa_start": 19,
"aa_end": null,
"aa_length": 676,
"cds_start": 57,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 2810,
"cdna_end": null,
"cdna_length": 5235,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCD",
"gene_hgnc_id": 9399,
"hgvs_c": "n.57C>T",
"hgvs_p": null,
"transcript": "ENST00000697588.1",
"protein_id": "ENSP00000513355.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2869,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCD",
"gene_hgnc_id": 9399,
"hgvs_c": "n.194C>T",
"hgvs_p": null,
"transcript": "XR_007095706.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1386,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PRKCD",
"gene_hgnc_id": 9399,
"dbsnp": "rs377115507",
"frequency_reference_population": 0.000042154596,
"hom_count_reference_population": 0,
"allele_count_reference_population": 68,
"gnomad_exomes_af": 0.0000431274,
"gnomad_genomes_af": 0.0000328252,
"gnomad_exomes_ac": 63,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7099999785423279,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.71,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -4.993,
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Benign",
"transcript": "NM_006254.4",
"gene_symbol": "PRKCD",
"hgnc_id": 9399,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.57C>T",
"hgvs_p": "p.Ala19Ala"
}
],
"clinvar_disease": " type III caused by mutation in PRKCD,Autoimmune lymphoproliferative syndrome",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Autoimmune lymphoproliferative syndrome, type III caused by mutation in PRKCD",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}