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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: 19-49862713-ATGGATATGGGCGTGCCGTCGT-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=49862713&ref=ATGGATATGGGCGTGCCGTCGT&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 49862713,
"ref": "ATGGATATGGGCGTGCCGTCGT",
"alt": "A",
"effect": "disruptive_inframe_deletion",
"transcript": "ENST00000322344.8",
"consequences": [
{
"aa_ref": "NDGTPISI",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.821_841delACGACGGCACGCCCATATCCA",
"hgvs_p": "p.Asn274_Ser280del",
"transcript": "NM_007254.4",
"protein_id": "NP_009185.2",
"transcript_support_level": null,
"aa_start": 274,
"aa_end": null,
"aa_length": 521,
"cds_start": 821,
"cds_end": null,
"cds_length": 1566,
"cdna_start": 962,
"cdna_end": null,
"cdna_length": 1731,
"mane_select": "ENST00000322344.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NDGTPISI",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.821_841delACGACGGCACGCCCATATCCA",
"hgvs_p": "p.Asn274_Ser280del",
"transcript": "ENST00000322344.8",
"protein_id": "ENSP00000323511.2",
"transcript_support_level": 1,
"aa_start": 274,
"aa_end": null,
"aa_length": 521,
"cds_start": 821,
"cds_end": null,
"cds_length": 1566,
"cdna_start": 962,
"cdna_end": null,
"cdna_length": 1731,
"mane_select": "NM_007254.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NDGTPISI",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.821_841delACGACGGCACGCCCATATCCA",
"hgvs_p": "p.Asn274_Ser280del",
"transcript": "ENST00000596014.5",
"protein_id": "ENSP00000472300.1",
"transcript_support_level": 1,
"aa_start": 274,
"aa_end": null,
"aa_length": 521,
"cds_start": 821,
"cds_end": null,
"cds_length": 1566,
"cdna_start": 923,
"cdna_end": null,
"cdna_length": 1665,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.*748_*768delACGACGGCACGCCCATATCCA",
"hgvs_p": null,
"transcript": "ENST00000593946.5",
"protein_id": "ENSP00000468896.1",
"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": 1723,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.*748_*768delACGACGGCACGCCCATATCCA",
"hgvs_p": null,
"transcript": "ENST00000593946.5",
"protein_id": "ENSP00000468896.1",
"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": 1723,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NDGTPISI",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.821_841delACGACGGCACGCCCATATCCA",
"hgvs_p": "p.Asn274_Ser280del",
"transcript": "ENST00000600573.5",
"protein_id": "ENSP00000469826.1",
"transcript_support_level": 5,
"aa_start": 274,
"aa_end": null,
"aa_length": 490,
"cds_start": 821,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 962,
"cdna_end": null,
"cdna_length": 1602,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NDGTPISI",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.713_733delACGACGGCACGCCCATATCCA",
"hgvs_p": "p.Asn238_Ser244del",
"transcript": "ENST00000631020.2",
"protein_id": "ENSP00000486707.1",
"transcript_support_level": 5,
"aa_start": 238,
"aa_end": null,
"aa_length": 485,
"cds_start": 713,
"cds_end": null,
"cds_length": 1458,
"cdna_start": 787,
"cdna_end": null,
"cdna_length": 1545,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NDGTPISI",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.821_841delACGACGGCACGCCCATATCCA",
"hgvs_p": "p.Asn274_Ser280del",
"transcript": "ENST00000600910.5",
"protein_id": "ENSP00000473137.1",
"transcript_support_level": 5,
"aa_start": 274,
"aa_end": null,
"aa_length": 455,
"cds_start": 821,
"cds_end": null,
"cds_length": 1368,
"cdna_start": 941,
"cdna_end": null,
"cdna_length": 1600,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "NDGTPISI",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.440_460delACGACGGCACGCCCATATCCA",
"hgvs_p": "p.Asn147_Ser153del",
"transcript": "ENST00000627317.1",
"protein_id": "ENSP00000486500.1",
"transcript_support_level": 5,
"aa_start": 147,
"aa_end": null,
"aa_length": 254,
"cds_start": 440,
"cds_end": null,
"cds_length": 765,
"cdna_start": 462,
"cdna_end": null,
"cdna_length": 767,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.176_196delACGACGGCACGCCCATATCCA",
"hgvs_p": null,
"transcript": "ENST00000593706.3",
"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": 849,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.1322_1342delACGACGGCACGCCCATATCCA",
"hgvs_p": null,
"transcript": "ENST00000594661.5",
"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": 2111,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.-2_19delACGACGGCACGCCCATATCCA",
"hgvs_p": null,
"transcript": "ENST00000625216.2",
"protein_id": "ENSP00000486898.1",
"transcript_support_level": 5,
"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": 629,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.*216_*236delACGACGGCACGCCCATATCCA",
"hgvs_p": null,
"transcript": "ENST00000627232.2",
"protein_id": "ENSP00000486037.1",
"transcript_support_level": 5,
"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": 1530,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.592_612delACGACGGCACGCCCATATCCA",
"hgvs_p": null,
"transcript": "ENST00000629179.1",
"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": 811,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.*216_*236delACGACGGCACGCCCATATCCA",
"hgvs_p": null,
"transcript": "ENST00000627232.2",
"protein_id": "ENSP00000486037.1",
"transcript_support_level": 5,
"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": 1530,
"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": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.-2_19delACGACGGCACGCCCATATCCA",
"hgvs_p": null,
"transcript": "ENST00000625216.2",
"protein_id": "ENSP00000486898.1",
"transcript_support_level": 5,
"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": 629,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.*67_*87delACGACGGCACGCCCATATCCA",
"hgvs_p": null,
"transcript": "ENST00000637325.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 100,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"dbsnp": "rs1555811217",
"frequency_reference_population": 0.0000013681556,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136816,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"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": 2.015,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM4",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000322344.8",
"gene_symbol": "PNKP",
"hgnc_id": 9154,
"effects": [
"disruptive_inframe_deletion"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.821_841delACGACGGCACGCCCATATCCA",
"hgvs_p": "p.Asn274_Ser280del"
}
],
"clinvar_disease": " 12,Developmental and epileptic encephalopathy,Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Developmental and epileptic encephalopathy, 12|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}