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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: 19-49861496-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=49861496&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 49861496,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000322344.8",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1401G>A",
"hgvs_p": "p.Thr467Thr",
"transcript": "NM_007254.4",
"protein_id": "NP_009185.2",
"transcript_support_level": null,
"aa_start": 467,
"aa_end": null,
"aa_length": 521,
"cds_start": 1401,
"cds_end": null,
"cds_length": 1566,
"cdna_start": 1522,
"cdna_end": null,
"cdna_length": 1731,
"mane_select": "ENST00000322344.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1401G>A",
"hgvs_p": "p.Thr467Thr",
"transcript": "ENST00000322344.8",
"protein_id": "ENSP00000323511.2",
"transcript_support_level": 1,
"aa_start": 467,
"aa_end": null,
"aa_length": 521,
"cds_start": 1401,
"cds_end": null,
"cds_length": 1566,
"cdna_start": 1522,
"cdna_end": null,
"cdna_length": 1731,
"mane_select": "NM_007254.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1401G>A",
"hgvs_p": "p.Thr467Thr",
"transcript": "ENST00000596014.5",
"protein_id": "ENSP00000472300.1",
"transcript_support_level": 1,
"aa_start": 467,
"aa_end": null,
"aa_length": 521,
"cds_start": 1401,
"cds_end": null,
"cds_length": 1566,
"cdna_start": 1483,
"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": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.*1328G>A",
"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": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.*1328G>A",
"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": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1291G>A",
"hgvs_p": "p.Gly431Arg",
"transcript": "ENST00000600910.5",
"protein_id": "ENSP00000473137.1",
"transcript_support_level": 5,
"aa_start": 431,
"aa_end": null,
"aa_length": 455,
"cds_start": 1291,
"cds_end": null,
"cds_length": 1368,
"cdna_start": 1391,
"cdna_end": null,
"cdna_length": 1600,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1308G>A",
"hgvs_p": "p.Thr436Thr",
"transcript": "ENST00000600573.5",
"protein_id": "ENSP00000469826.1",
"transcript_support_level": 5,
"aa_start": 436,
"aa_end": null,
"aa_length": 490,
"cds_start": 1308,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 1429,
"cdna_end": null,
"cdna_length": 1602,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1293G>A",
"hgvs_p": "p.Thr431Thr",
"transcript": "ENST00000631020.2",
"protein_id": "ENSP00000486707.1",
"transcript_support_level": 5,
"aa_start": 431,
"aa_end": null,
"aa_length": 485,
"cds_start": 1293,
"cds_end": null,
"cds_length": 1458,
"cdna_start": 1347,
"cdna_end": null,
"cdna_length": 1545,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.108G>A",
"hgvs_p": "p.Thr36Thr",
"transcript": "ENST00000597965.2",
"protein_id": "ENSP00000471097.2",
"transcript_support_level": 5,
"aa_start": 36,
"aa_end": null,
"aa_length": 56,
"cds_start": 108,
"cds_end": null,
"cds_length": 171,
"cdna_start": 108,
"cdna_end": null,
"cdna_length": 351,
"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": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.1902G>A",
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.304G>A",
"hgvs_p": null,
"transcript": "ENST00000595081.5",
"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": 513,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.321G>A",
"hgvs_p": null,
"transcript": "ENST00000599454.5",
"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": 529,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.473G>A",
"hgvs_p": null,
"transcript": "ENST00000601816.3",
"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": 682,
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.*218G>A",
"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": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.*796G>A",
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.6G>A",
"hgvs_p": null,
"transcript": "ENST00000640501.1",
"protein_id": "ENSP00000491347.1",
"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": 151,
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.*218G>A",
"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": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.*796G>A",
"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": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.57+112G>A",
"hgvs_p": null,
"transcript": "ENST00000636840.1",
"protein_id": "ENSP00000490737.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 37,
"cds_start": -4,
"cds_end": null,
"cds_length": 115,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 117,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"dbsnp": "rs374547164",
"frequency_reference_population": 0.00004591015,
"hom_count_reference_population": 0,
"allele_count_reference_population": 74,
"gnomad_exomes_af": 0.0000465439,
"gnomad_genomes_af": 0.0000397725,
"gnomad_exomes_ac": 68,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.10128054022789001,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": 0.0848,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.38,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -6.245,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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": -11,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7",
"acmg_by_gene": [
{
"score": -11,
"benign_score": 11,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7"
],
"verdict": "Benign",
"transcript": "ENST00000322344.8",
"gene_symbol": "PNKP",
"hgnc_id": 9154,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1401G>A",
"hgvs_p": "p.Thr467Thr"
}
],
"clinvar_disease": " 12,Developmental and epileptic encephalopathy,Inborn genetic diseases,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:1",
"phenotype_combined": "Developmental and epileptic encephalopathy, 12|not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}