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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: 1-233198986-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=233198986&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 233198986,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_014801.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.3019G>T",
"hgvs_p": "p.Val1007Phe",
"transcript": "NM_014801.4",
"protein_id": "NP_055616.3",
"transcript_support_level": null,
"aa_start": 1007,
"aa_end": null,
"aa_length": 2137,
"cds_start": 3019,
"cds_end": null,
"cds_length": 6414,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000258229.14",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_014801.4"
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.3019G>T",
"hgvs_p": "p.Val1007Phe",
"transcript": "ENST00000258229.14",
"protein_id": "ENSP00000258229.8",
"transcript_support_level": 5,
"aa_start": 1007,
"aa_end": null,
"aa_length": 2137,
"cds_start": 3019,
"cds_end": null,
"cds_length": 6414,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_014801.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000258229.14"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "n.*509G>T",
"hgvs_p": null,
"transcript": "ENST00000475463.6",
"protein_id": "ENSP00000429360.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000475463.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "n.*509G>T",
"hgvs_p": null,
"transcript": "ENST00000475463.6",
"protein_id": "ENSP00000429360.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000475463.6"
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.418G>T",
"hgvs_p": "p.Val140Phe",
"transcript": "ENST00000488780.6",
"protein_id": "ENSP00000430820.1",
"transcript_support_level": 5,
"aa_start": 140,
"aa_end": null,
"aa_length": 424,
"cds_start": 418,
"cds_end": null,
"cds_length": 1275,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000488780.6"
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.526G>T",
"hgvs_p": "p.Val176Phe",
"transcript": "ENST00000518351.2",
"protein_id": "ENSP00000429231.1",
"transcript_support_level": 4,
"aa_start": 176,
"aa_end": null,
"aa_length": 180,
"cds_start": 526,
"cds_end": null,
"cds_length": 545,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000518351.2"
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.2770G>T",
"hgvs_p": "p.Val924Phe",
"transcript": "XM_047430870.1",
"protein_id": "XP_047286826.1",
"transcript_support_level": null,
"aa_start": 924,
"aa_end": null,
"aa_length": 2054,
"cds_start": 2770,
"cds_end": null,
"cds_length": 6165,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047430870.1"
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.2410G>T",
"hgvs_p": "p.Val804Phe",
"transcript": "XM_047430871.1",
"protein_id": "XP_047286827.1",
"transcript_support_level": null,
"aa_start": 804,
"aa_end": null,
"aa_length": 1934,
"cds_start": 2410,
"cds_end": null,
"cds_length": 5805,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047430871.1"
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.3019G>T",
"hgvs_p": "p.Val1007Phe",
"transcript": "XM_047430872.1",
"protein_id": "XP_047286828.1",
"transcript_support_level": null,
"aa_start": 1007,
"aa_end": null,
"aa_length": 1468,
"cds_start": 3019,
"cds_end": null,
"cds_length": 4407,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047430872.1"
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.793G>T",
"hgvs_p": "p.Val265Phe",
"transcript": "XM_011544278.3",
"protein_id": "XP_011542580.2",
"transcript_support_level": null,
"aa_start": 265,
"aa_end": null,
"aa_length": 1395,
"cds_start": 793,
"cds_end": null,
"cds_length": 4188,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011544278.3"
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.3019G>T",
"hgvs_p": "p.Val1007Phe",
"transcript": "XM_006711816.4",
"protein_id": "XP_006711879.1",
"transcript_support_level": null,
"aa_start": 1007,
"aa_end": null,
"aa_length": 1364,
"cds_start": 3019,
"cds_end": null,
"cds_length": 4095,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006711816.4"
},
{
"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": 31,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "c.2691+18913G>T",
"hgvs_p": null,
"transcript": "ENST00000912675.1",
"protein_id": "ENSP00000582734.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2012,
"cds_start": null,
"cds_end": null,
"cds_length": 6039,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912675.1"
},
{
"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": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "n.82G>T",
"hgvs_p": null,
"transcript": "ENST00000462233.5",
"protein_id": "ENSP00000428488.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000462233.5"
},
{
"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": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "n.3266G>T",
"hgvs_p": null,
"transcript": "XR_001737430.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_001737430.2"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"hgvs_c": "n.*204G>T",
"hgvs_p": null,
"transcript": "ENST00000517808.1",
"protein_id": "ENSP00000429262.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000517808.1"
}
],
"gene_symbol": "PCNX2",
"gene_hgnc_id": 8736,
"dbsnp": "rs535193160",
"frequency_reference_population": 0.0000061924193,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000619242,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.03968098759651184,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.288,
"revel_prediction": "Benign",
"alphamissense_score": 0.0663,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.44,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.144,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.05,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_014801.4",
"gene_symbol": "PCNX2",
"hgnc_id": 8736,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3019G>T",
"hgvs_p": "p.Val1007Phe"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}