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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: 12-110327725-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=110327725&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 110327725,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000539276.7",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A2",
"gene_hgnc_id": 812,
"hgvs_c": "c.803G>T",
"hgvs_p": "p.Cys268Phe",
"transcript": "NM_170665.4",
"protein_id": "NP_733765.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 1042,
"cds_start": 803,
"cds_end": null,
"cds_length": 3129,
"cdna_start": 1346,
"cdna_end": null,
"cdna_length": 8295,
"mane_select": "ENST00000539276.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A2",
"gene_hgnc_id": 812,
"hgvs_c": "c.803G>T",
"hgvs_p": "p.Cys268Phe",
"transcript": "ENST00000539276.7",
"protein_id": "ENSP00000440045.2",
"transcript_support_level": 1,
"aa_start": 268,
"aa_end": null,
"aa_length": 1042,
"cds_start": 803,
"cds_end": null,
"cds_length": 3129,
"cdna_start": 1346,
"cdna_end": null,
"cdna_length": 8295,
"mane_select": "NM_170665.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A2",
"gene_hgnc_id": 812,
"hgvs_c": "c.803G>T",
"hgvs_p": "p.Cys268Phe",
"transcript": "ENST00000308664.10",
"protein_id": "ENSP00000311186.6",
"transcript_support_level": 1,
"aa_start": 268,
"aa_end": null,
"aa_length": 997,
"cds_start": 803,
"cds_end": null,
"cds_length": 2994,
"cdna_start": 1477,
"cdna_end": null,
"cdna_length": 4453,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A2",
"gene_hgnc_id": 812,
"hgvs_c": "c.698G>T",
"hgvs_p": "p.Cys233Phe",
"transcript": "NM_001413013.1",
"protein_id": "NP_001399942.1",
"transcript_support_level": null,
"aa_start": 233,
"aa_end": null,
"aa_length": 1007,
"cds_start": 698,
"cds_end": null,
"cds_length": 3024,
"cdna_start": 1241,
"cdna_end": null,
"cdna_length": 8190,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "F",
"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": "ATP2A2",
"gene_hgnc_id": 812,
"hgvs_c": "c.803G>T",
"hgvs_p": "p.Cys268Phe",
"transcript": "NM_001413014.1",
"protein_id": "NP_001399943.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 999,
"cds_start": 803,
"cds_end": null,
"cds_length": 3000,
"cdna_start": 1346,
"cdna_end": null,
"cdna_length": 4386,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A2",
"gene_hgnc_id": 812,
"hgvs_c": "c.803G>T",
"hgvs_p": "p.Cys268Phe",
"transcript": "NM_001681.4",
"protein_id": "NP_001672.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 997,
"cds_start": 803,
"cds_end": null,
"cds_length": 2994,
"cdna_start": 1346,
"cdna_end": null,
"cdna_length": 4325,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A2",
"gene_hgnc_id": 812,
"hgvs_c": "c.473G>T",
"hgvs_p": "p.Cys158Phe",
"transcript": "ENST00000548169.2",
"protein_id": "ENSP00000449454.2",
"transcript_support_level": 2,
"aa_start": 158,
"aa_end": null,
"aa_length": 932,
"cds_start": 473,
"cds_end": null,
"cds_length": 2799,
"cdna_start": 474,
"cdna_end": null,
"cdna_length": 2951,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A2",
"gene_hgnc_id": 812,
"hgvs_c": "c.428G>T",
"hgvs_p": "p.Cys143Phe",
"transcript": "NM_001413015.1",
"protein_id": "NP_001399944.1",
"transcript_support_level": null,
"aa_start": 143,
"aa_end": null,
"aa_length": 917,
"cds_start": 428,
"cds_end": null,
"cds_length": 2754,
"cdna_start": 1034,
"cdna_end": null,
"cdna_length": 7983,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A2",
"gene_hgnc_id": 812,
"hgvs_c": "c.803G>T",
"hgvs_p": "p.Cys268Phe",
"transcript": "XM_011538402.4",
"protein_id": "XP_011536704.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 999,
"cds_start": 803,
"cds_end": null,
"cds_length": 3000,
"cdna_start": 1346,
"cdna_end": null,
"cdna_length": 7224,
"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": 7,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A2",
"gene_hgnc_id": 812,
"hgvs_c": "n.*643G>T",
"hgvs_p": null,
"transcript": "ENST00000377685.9",
"protein_id": "ENSP00000366913.4",
"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": 5702,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A2",
"gene_hgnc_id": 812,
"hgvs_c": "n.848G>T",
"hgvs_p": null,
"transcript": "ENST00000547050.1",
"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": 1176,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A2",
"gene_hgnc_id": 812,
"hgvs_c": "n.39G>T",
"hgvs_p": null,
"transcript": "ENST00000549840.1",
"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": 503,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A2",
"gene_hgnc_id": 812,
"hgvs_c": "n.*643G>T",
"hgvs_p": null,
"transcript": "ENST00000377685.9",
"protein_id": "ENSP00000366913.4",
"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": 5702,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATP2A2",
"gene_hgnc_id": 812,
"dbsnp": "rs121912733",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9249565005302429,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.18000000715255737,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.895,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9963,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.42,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.926,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.18,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP2,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP2",
"PP3_Moderate",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000539276.7",
"gene_symbol": "ATP2A2",
"hgnc_id": 812,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.803G>T",
"hgvs_p": "p.Cys268Phe"
}
],
"clinvar_disease": " acral hemorrhagic type,Darier disease",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Darier disease, acral hemorrhagic type",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}