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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: 9-128713304-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=128713304&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 128713304,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000291906.5",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKN3",
"gene_hgnc_id": 17999,
"hgvs_c": "c.1009G>C",
"hgvs_p": "p.Asp337His",
"transcript": "NM_013355.5",
"protein_id": "NP_037487.2",
"transcript_support_level": null,
"aa_start": 337,
"aa_end": null,
"aa_length": 889,
"cds_start": 1009,
"cds_end": null,
"cds_length": 2670,
"cdna_start": 1422,
"cdna_end": null,
"cdna_length": 3393,
"mane_select": "ENST00000291906.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKN3",
"gene_hgnc_id": 17999,
"hgvs_c": "c.1009G>C",
"hgvs_p": "p.Asp337His",
"transcript": "ENST00000291906.5",
"protein_id": "ENSP00000291906.4",
"transcript_support_level": 1,
"aa_start": 337,
"aa_end": null,
"aa_length": 889,
"cds_start": 1009,
"cds_end": null,
"cds_length": 2670,
"cdna_start": 1422,
"cdna_end": null,
"cdna_length": 3393,
"mane_select": "NM_013355.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKN3",
"gene_hgnc_id": 17999,
"hgvs_c": "c.1009G>C",
"hgvs_p": "p.Asp337His",
"transcript": "NM_001317926.2",
"protein_id": "NP_001304855.1",
"transcript_support_level": null,
"aa_start": 337,
"aa_end": null,
"aa_length": 833,
"cds_start": 1009,
"cds_end": null,
"cds_length": 2502,
"cdna_start": 1422,
"cdna_end": null,
"cdna_length": 3349,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKN3",
"gene_hgnc_id": 17999,
"hgvs_c": "c.1030G>C",
"hgvs_p": "p.Asp344His",
"transcript": "XM_006717080.4",
"protein_id": "XP_006717143.1",
"transcript_support_level": null,
"aa_start": 344,
"aa_end": null,
"aa_length": 896,
"cds_start": 1030,
"cds_end": null,
"cds_length": 2691,
"cdna_start": 1598,
"cdna_end": null,
"cdna_length": 3569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKN3",
"gene_hgnc_id": 17999,
"hgvs_c": "c.1000G>C",
"hgvs_p": "p.Asp334His",
"transcript": "XM_005251946.4",
"protein_id": "XP_005252003.1",
"transcript_support_level": null,
"aa_start": 334,
"aa_end": null,
"aa_length": 886,
"cds_start": 1000,
"cds_end": null,
"cds_length": 2661,
"cdna_start": 2258,
"cdna_end": null,
"cdna_length": 4229,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKN3",
"gene_hgnc_id": 17999,
"hgvs_c": "c.1030G>C",
"hgvs_p": "p.Asp344His",
"transcript": "XM_017014649.3",
"protein_id": "XP_016870138.1",
"transcript_support_level": null,
"aa_start": 344,
"aa_end": null,
"aa_length": 840,
"cds_start": 1030,
"cds_end": null,
"cds_length": 2523,
"cdna_start": 1598,
"cdna_end": null,
"cdna_length": 3525,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKN3",
"gene_hgnc_id": 17999,
"hgvs_c": "c.631G>C",
"hgvs_p": "p.Asp211His",
"transcript": "XM_017014650.2",
"protein_id": "XP_016870139.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 763,
"cds_start": 631,
"cds_end": null,
"cds_length": 2292,
"cdna_start": 1624,
"cdna_end": null,
"cdna_length": 3595,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKN3",
"gene_hgnc_id": 17999,
"hgvs_c": "c.631G>C",
"hgvs_p": "p.Asp211His",
"transcript": "XM_047423278.1",
"protein_id": "XP_047279234.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 763,
"cds_start": 631,
"cds_end": null,
"cds_length": 2292,
"cdna_start": 1083,
"cdna_end": null,
"cdna_length": 3054,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKN3",
"gene_hgnc_id": 17999,
"hgvs_c": "c.631G>C",
"hgvs_p": "p.Asp211His",
"transcript": "XM_047423279.1",
"protein_id": "XP_047279235.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 763,
"cds_start": 631,
"cds_end": null,
"cds_length": 2292,
"cdna_start": 1395,
"cdna_end": null,
"cdna_length": 3366,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKN3",
"gene_hgnc_id": 17999,
"hgvs_c": "n.109G>C",
"hgvs_p": null,
"transcript": "ENST00000483521.1",
"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": 597,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PKN3",
"gene_hgnc_id": 17999,
"dbsnp": "rs72758841",
"frequency_reference_population": 0.000035313402,
"hom_count_reference_population": 0,
"allele_count_reference_population": 57,
"gnomad_exomes_af": 0.0000383102,
"gnomad_genomes_af": 0.00000656314,
"gnomad_exomes_ac": 56,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8501150012016296,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.2199999988079071,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.654,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.7561,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.18,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.602,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.22,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000291906.5",
"gene_symbol": "PKN3",
"hgnc_id": 17999,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1009G>C",
"hgvs_p": "p.Asp337His"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}