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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: 19-11447525-AGAGGAGGAGGAG-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=11447525&ref=AGAGGAGGAGGAG&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 11447525,
"ref": "AGAGGAGGAGGAG",
"alt": "A",
"effect": "disruptive_inframe_deletion",
"transcript": "ENST00000677123.1",
"consequences": [
{
"aa_ref": "EEEEE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCSH",
"gene_hgnc_id": 9411,
"hgvs_c": "c.957_968delGGAGGAGGAGGA",
"hgvs_p": "p.Glu320_Glu323del",
"transcript": "NM_001289104.2",
"protein_id": "NP_001276033.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 535,
"cds_start": 957,
"cds_end": null,
"cds_length": 1608,
"cdna_start": 1106,
"cdna_end": null,
"cdna_length": 2096,
"mane_select": "ENST00000677123.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "EEEEE",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCSH",
"gene_hgnc_id": 9411,
"hgvs_c": "c.957_968delGGAGGAGGAGGA",
"hgvs_p": "p.Glu320_Glu323del",
"transcript": "ENST00000677123.1",
"protein_id": "ENSP00000503163.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 535,
"cds_start": 957,
"cds_end": null,
"cds_length": 1608,
"cdna_start": 1106,
"cdna_end": null,
"cdna_length": 2096,
"mane_select": "NM_001289104.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "EEEEE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCSH",
"gene_hgnc_id": 9411,
"hgvs_c": "c.957_968delGGAGGAGGAGGA",
"hgvs_p": "p.Glu320_Glu323del",
"transcript": "ENST00000592741.5",
"protein_id": "ENSP00000466134.1",
"transcript_support_level": 1,
"aa_start": 319,
"aa_end": null,
"aa_length": 535,
"cds_start": 957,
"cds_end": null,
"cds_length": 1608,
"cdna_start": 1110,
"cdna_end": null,
"cdna_length": 2100,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "EEEEE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCSH",
"gene_hgnc_id": 9411,
"hgvs_c": "c.957_968delGGAGGAGGAGGA",
"hgvs_p": "p.Glu320_Glu323del",
"transcript": "ENST00000589838.5",
"protein_id": "ENSP00000465461.1",
"transcript_support_level": 1,
"aa_start": 319,
"aa_end": null,
"aa_length": 528,
"cds_start": 957,
"cds_end": null,
"cds_length": 1587,
"cdna_start": 957,
"cdna_end": null,
"cdna_length": 1898,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "EEEEE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCSH",
"gene_hgnc_id": 9411,
"hgvs_c": "c.957_968delGGAGGAGGAGGA",
"hgvs_p": "p.Glu320_Glu323del",
"transcript": "NM_001289103.2",
"protein_id": "NP_001276032.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 535,
"cds_start": 957,
"cds_end": null,
"cds_length": 1608,
"cdna_start": 1110,
"cdna_end": null,
"cdna_length": 2100,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "EEEEE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCSH",
"gene_hgnc_id": 9411,
"hgvs_c": "c.957_968delGGAGGAGGAGGA",
"hgvs_p": "p.Glu320_Glu323del",
"transcript": "NM_001379608.1",
"protein_id": "NP_001366537.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 528,
"cds_start": 957,
"cds_end": null,
"cds_length": 1587,
"cdna_start": 1110,
"cdna_end": null,
"cdna_length": 2079,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "EEEEE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCSH",
"gene_hgnc_id": 9411,
"hgvs_c": "c.957_968delGGAGGAGGAGGA",
"hgvs_p": "p.Glu320_Glu323del",
"transcript": "NM_002743.3",
"protein_id": "NP_002734.2",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 528,
"cds_start": 957,
"cds_end": null,
"cds_length": 1587,
"cdna_start": 1096,
"cdna_end": null,
"cdna_length": 2065,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "EEEEE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCSH",
"gene_hgnc_id": 9411,
"hgvs_c": "c.957_968delGGAGGAGGAGGA",
"hgvs_p": "p.Glu320_Glu323del",
"transcript": "NM_001001329.3",
"protein_id": "NP_001001329.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 525,
"cds_start": 957,
"cds_end": null,
"cds_length": 1578,
"cdna_start": 1106,
"cdna_end": null,
"cdna_length": 2066,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "EEEEE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCSH",
"gene_hgnc_id": 9411,
"hgvs_c": "c.957_968delGGAGGAGGAGGA",
"hgvs_p": "p.Glu320_Glu323del",
"transcript": "NM_001289102.2",
"protein_id": "NP_001276031.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 525,
"cds_start": 957,
"cds_end": null,
"cds_length": 1578,
"cdna_start": 1002,
"cdna_end": null,
"cdna_length": 1962,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "EEEEE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCSH",
"gene_hgnc_id": 9411,
"hgvs_c": "c.957_968delGGAGGAGGAGGA",
"hgvs_p": "p.Glu320_Glu323del",
"transcript": "NM_001379609.1",
"protein_id": "NP_001366538.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 525,
"cds_start": 957,
"cds_end": null,
"cds_length": 1578,
"cdna_start": 1110,
"cdna_end": null,
"cdna_length": 2070,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "EEEEE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCSH",
"gene_hgnc_id": 9411,
"hgvs_c": "c.957_968delGGAGGAGGAGGA",
"hgvs_p": "p.Glu320_Glu323del",
"transcript": "ENST00000587327.5",
"protein_id": "ENSP00000466012.1",
"transcript_support_level": 2,
"aa_start": 319,
"aa_end": null,
"aa_length": 525,
"cds_start": 957,
"cds_end": null,
"cds_length": 1578,
"cdna_start": 1330,
"cdna_end": null,
"cdna_length": 2189,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "EEEEE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCSH",
"gene_hgnc_id": 9411,
"hgvs_c": "c.957_968delGGAGGAGGAGGA",
"hgvs_p": "p.Glu320_Glu323del",
"transcript": "ENST00000591462.6",
"protein_id": "ENSP00000465489.1",
"transcript_support_level": 5,
"aa_start": 319,
"aa_end": null,
"aa_length": 525,
"cds_start": 957,
"cds_end": null,
"cds_length": 1578,
"cdna_start": 1106,
"cdna_end": null,
"cdna_length": 2063,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCSH",
"gene_hgnc_id": 9411,
"hgvs_c": "n.230_241delGGAGGAGGAGGA",
"hgvs_p": null,
"transcript": "ENST00000585325.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 598,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCSH",
"gene_hgnc_id": 9411,
"hgvs_c": "n.148_159delGGAGGAGGAGGA",
"hgvs_p": null,
"transcript": "ENST00000585540.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 501,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCSH",
"gene_hgnc_id": 9411,
"hgvs_c": "n.204_215delGGAGGAGGAGGA",
"hgvs_p": null,
"transcript": "ENST00000592445.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 598,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKCSH",
"gene_hgnc_id": 9411,
"hgvs_c": "n.-39_-28delGAGGAGGAGGAG",
"hgvs_p": null,
"transcript": "ENST00000586486.1",
"protein_id": "ENSP00000465948.1",
"transcript_support_level": 1,
"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": 1613,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PRKCSH",
"gene_hgnc_id": 9411,
"dbsnp": "rs3217229",
"frequency_reference_population": 0.00016099318,
"hom_count_reference_population": 1,
"allele_count_reference_population": 255,
"gnomad_exomes_af": 0.000165936,
"gnomad_genomes_af": 0.000113617,
"gnomad_exomes_ac": 238,
"gnomad_genomes_ac": 17,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 3.273,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -17,
"acmg_classification": "Benign",
"acmg_criteria": "BP3,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -17,
"benign_score": 17,
"pathogenic_score": 0,
"criteria": [
"BP3",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000677123.1",
"gene_symbol": "PRKCSH",
"hgnc_id": 9411,
"effects": [
"disruptive_inframe_deletion"
],
"inheritance_mode": "AD",
"hgvs_c": "c.957_968delGGAGGAGGAGGA",
"hgvs_p": "p.Glu320_Glu323del"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}