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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: 16-28898046-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=28898046&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 28898046,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000395503.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A1",
"gene_hgnc_id": 811,
"hgvs_c": "c.1466G>A",
"hgvs_p": "p.Arg489Gln",
"transcript": "NM_004320.6",
"protein_id": "NP_004311.1",
"transcript_support_level": null,
"aa_start": 489,
"aa_end": null,
"aa_length": 994,
"cds_start": 1466,
"cds_end": null,
"cds_length": 2985,
"cdna_start": 1650,
"cdna_end": null,
"cdna_length": 3493,
"mane_select": "ENST00000395503.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A1",
"gene_hgnc_id": 811,
"hgvs_c": "c.1466G>A",
"hgvs_p": "p.Arg489Gln",
"transcript": "ENST00000395503.9",
"protein_id": "ENSP00000378879.5",
"transcript_support_level": 1,
"aa_start": 489,
"aa_end": null,
"aa_length": 994,
"cds_start": 1466,
"cds_end": null,
"cds_length": 2985,
"cdna_start": 1650,
"cdna_end": null,
"cdna_length": 3493,
"mane_select": "NM_004320.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A1",
"gene_hgnc_id": 811,
"hgvs_c": "c.1466G>A",
"hgvs_p": "p.Arg489Gln",
"transcript": "NM_173201.5",
"protein_id": "NP_775293.1",
"transcript_support_level": null,
"aa_start": 489,
"aa_end": null,
"aa_length": 1001,
"cds_start": 1466,
"cds_end": null,
"cds_length": 3006,
"cdna_start": 1650,
"cdna_end": null,
"cdna_length": 3451,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A1",
"gene_hgnc_id": 811,
"hgvs_c": "c.1466G>A",
"hgvs_p": "p.Arg489Gln",
"transcript": "ENST00000357084.7",
"protein_id": "ENSP00000349595.3",
"transcript_support_level": 2,
"aa_start": 489,
"aa_end": null,
"aa_length": 1001,
"cds_start": 1466,
"cds_end": null,
"cds_length": 3006,
"cdna_start": 1733,
"cdna_end": null,
"cdna_length": 3532,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A1",
"gene_hgnc_id": 811,
"hgvs_c": "c.1091G>A",
"hgvs_p": "p.Arg364Gln",
"transcript": "NM_001286075.2",
"protein_id": "NP_001273004.1",
"transcript_support_level": null,
"aa_start": 364,
"aa_end": null,
"aa_length": 869,
"cds_start": 1091,
"cds_end": null,
"cds_length": 2610,
"cdna_start": 1299,
"cdna_end": null,
"cdna_length": 3142,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A1",
"gene_hgnc_id": 811,
"hgvs_c": "c.1091G>A",
"hgvs_p": "p.Arg364Gln",
"transcript": "ENST00000536376.5",
"protein_id": "ENSP00000443101.1",
"transcript_support_level": 2,
"aa_start": 364,
"aa_end": null,
"aa_length": 869,
"cds_start": 1091,
"cds_end": null,
"cds_length": 2610,
"cdna_start": 1289,
"cdna_end": null,
"cdna_length": 3130,
"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": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A1",
"gene_hgnc_id": 811,
"hgvs_c": "n.*109G>A",
"hgvs_p": null,
"transcript": "ENST00000564732.1",
"protein_id": "ENSP00000457357.1",
"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": 831,
"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": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A1",
"gene_hgnc_id": 811,
"hgvs_c": "n.*109G>A",
"hgvs_p": null,
"transcript": "ENST00000564732.1",
"protein_id": "ENSP00000457357.1",
"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": 831,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATP2A1",
"gene_hgnc_id": 811,
"dbsnp": "rs868448815",
"frequency_reference_population": 0.000025402884,
"hom_count_reference_population": 0,
"allele_count_reference_population": 41,
"gnomad_exomes_af": 0.0000239418,
"gnomad_genomes_af": 0.0000394446,
"gnomad_exomes_ac": 35,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.850251317024231,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.812,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9937,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.29,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.998,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM1",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000395503.9",
"gene_symbol": "ATP2A1",
"hgnc_id": 811,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1466G>A",
"hgvs_p": "p.Arg489Gln"
}
],
"clinvar_disease": "Brody myopathy,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:4",
"phenotype_combined": "not specified|Brody myopathy|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}