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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: 16-28902318-G-GC (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=28902318&ref=G&alt=GC&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 28902318,
"ref": "G",
"alt": "GC",
"effect": "frameshift_variant",
"transcript": "NM_173201.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A1",
"gene_hgnc_id": 811,
"hgvs_c": "c.2464dupC",
"hgvs_p": "p.Arg822fs",
"transcript": "NM_004320.6",
"protein_id": "NP_004311.1",
"transcript_support_level": null,
"aa_start": 822,
"aa_end": null,
"aa_length": 994,
"cds_start": 2465,
"cds_end": null,
"cds_length": 2985,
"cdna_start": 2649,
"cdna_end": null,
"cdna_length": 3493,
"mane_select": "ENST00000395503.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004320.6"
},
{
"aa_ref": "R",
"aa_alt": "P?",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A1",
"gene_hgnc_id": 811,
"hgvs_c": "c.2464dupC",
"hgvs_p": "p.Arg822fs",
"transcript": "ENST00000395503.9",
"protein_id": "ENSP00000378879.5",
"transcript_support_level": 1,
"aa_start": 822,
"aa_end": null,
"aa_length": 994,
"cds_start": 2465,
"cds_end": null,
"cds_length": 2985,
"cdna_start": 2649,
"cdna_end": null,
"cdna_length": 3493,
"mane_select": "NM_004320.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000395503.9"
},
{
"aa_ref": "R",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A1",
"gene_hgnc_id": 811,
"hgvs_c": "c.2497dupC",
"hgvs_p": "p.Arg833fs",
"transcript": "ENST00000971328.1",
"protein_id": "ENSP00000641387.1",
"transcript_support_level": null,
"aa_start": 833,
"aa_end": null,
"aa_length": 1005,
"cds_start": 2498,
"cds_end": null,
"cds_length": 3018,
"cdna_start": 2682,
"cdna_end": null,
"cdna_length": 3522,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971328.1"
},
{
"aa_ref": "R",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A1",
"gene_hgnc_id": 811,
"hgvs_c": "c.2464dupC",
"hgvs_p": "p.Arg822fs",
"transcript": "NM_173201.5",
"protein_id": "NP_775293.1",
"transcript_support_level": null,
"aa_start": 822,
"aa_end": null,
"aa_length": 1001,
"cds_start": 2465,
"cds_end": null,
"cds_length": 3006,
"cdna_start": 2649,
"cdna_end": null,
"cdna_length": 3451,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_173201.5"
},
{
"aa_ref": "R",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A1",
"gene_hgnc_id": 811,
"hgvs_c": "c.2464dupC",
"hgvs_p": "p.Arg822fs",
"transcript": "ENST00000357084.7",
"protein_id": "ENSP00000349595.3",
"transcript_support_level": 2,
"aa_start": 822,
"aa_end": null,
"aa_length": 1001,
"cds_start": 2465,
"cds_end": null,
"cds_length": 3006,
"cdna_start": 2732,
"cdna_end": null,
"cdna_length": 3532,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000357084.7"
},
{
"aa_ref": "R",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A1",
"gene_hgnc_id": 811,
"hgvs_c": "c.2464dupC",
"hgvs_p": "p.Arg822fs",
"transcript": "ENST00000971325.1",
"protein_id": "ENSP00000641384.1",
"transcript_support_level": null,
"aa_start": 822,
"aa_end": null,
"aa_length": 994,
"cds_start": 2465,
"cds_end": null,
"cds_length": 2985,
"cdna_start": 2649,
"cdna_end": null,
"cdna_length": 3487,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971325.1"
},
{
"aa_ref": "R",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A1",
"gene_hgnc_id": 811,
"hgvs_c": "c.2446dupC",
"hgvs_p": "p.Arg816fs",
"transcript": "ENST00000971329.1",
"protein_id": "ENSP00000641388.1",
"transcript_support_level": null,
"aa_start": 816,
"aa_end": null,
"aa_length": 988,
"cds_start": 2447,
"cds_end": null,
"cds_length": 2967,
"cdna_start": 2626,
"cdna_end": null,
"cdna_length": 3468,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971329.1"
},
{
"aa_ref": "R",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A1",
"gene_hgnc_id": 811,
"hgvs_c": "c.2383dupC",
"hgvs_p": "p.Arg795fs",
"transcript": "ENST00000971326.1",
"protein_id": "ENSP00000641385.1",
"transcript_support_level": null,
"aa_start": 795,
"aa_end": null,
"aa_length": 967,
"cds_start": 2384,
"cds_end": null,
"cds_length": 2904,
"cdna_start": 2568,
"cdna_end": null,
"cdna_length": 3411,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971326.1"
},
{
"aa_ref": "R",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A1",
"gene_hgnc_id": 811,
"hgvs_c": "c.2365dupC",
"hgvs_p": "p.Arg789fs",
"transcript": "ENST00000971327.1",
"protein_id": "ENSP00000641386.1",
"transcript_support_level": null,
"aa_start": 789,
"aa_end": null,
"aa_length": 961,
"cds_start": 2366,
"cds_end": null,
"cds_length": 2886,
"cdna_start": 2549,
"cdna_end": null,
"cdna_length": 3391,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971327.1"
},
{
"aa_ref": "R",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A1",
"gene_hgnc_id": 811,
"hgvs_c": "c.2089dupC",
"hgvs_p": "p.Arg697fs",
"transcript": "NM_001286075.2",
"protein_id": "NP_001273004.1",
"transcript_support_level": null,
"aa_start": 697,
"aa_end": null,
"aa_length": 869,
"cds_start": 2090,
"cds_end": null,
"cds_length": 2610,
"cdna_start": 2298,
"cdna_end": null,
"cdna_length": 3142,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001286075.2"
},
{
"aa_ref": "R",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A1",
"gene_hgnc_id": 811,
"hgvs_c": "c.2089dupC",
"hgvs_p": "p.Arg697fs",
"transcript": "ENST00000536376.5",
"protein_id": "ENSP00000443101.1",
"transcript_support_level": 2,
"aa_start": 697,
"aa_end": null,
"aa_length": 869,
"cds_start": 2090,
"cds_end": null,
"cds_length": 2610,
"cdna_start": 2288,
"cdna_end": null,
"cdna_length": 3130,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000536376.5"
}
],
"gene_symbol": "ATP2A1",
"gene_hgnc_id": 811,
"dbsnp": "rs751365374",
"frequency_reference_population": 0.00024192978,
"hom_count_reference_population": 0,
"allele_count_reference_population": 390,
"gnomad_exomes_af": 0.000253337,
"gnomad_genomes_af": 0.000131985,
"gnomad_exomes_ac": 370,
"gnomad_genomes_ac": 20,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 0.14,
"phylop100way_prediction": "Benign",
"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": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PVS1",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_173201.5",
"gene_symbol": "ATP2A1",
"hgnc_id": 811,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.2464dupC",
"hgvs_p": "p.Arg822fs"
}
],
"clinvar_disease": "ATP2A1-related disorder,Brody myopathy,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:5 LP:2 O:1",
"phenotype_combined": "Brody myopathy|not provided|ATP2A1-related disorder",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}