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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: 16-28902591-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=28902591&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 13,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ATP2A1",
"hgnc_id": 811,
"hgvs_c": "c.2536G>A",
"hgvs_p": "p.Ala846Thr",
"inheritance_mode": "AR,AD",
"pathogenic_score": 0,
"score": -13,
"transcript": "NM_173201.5",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_score": -13,
"allele_count_reference_population": 666,
"alphamissense_prediction": null,
"alphamissense_score": 0.1103,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.06,
"chr": "16",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Brody myopathy,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1 B:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.011756062507629395,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 994,
"aa_ref": "A",
"aa_start": 846,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3493,
"cdna_start": 2720,
"cds_end": null,
"cds_length": 2985,
"cds_start": 2536,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_004320.6",
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"hgvs_c": "c.2536G>A",
"hgvs_p": "p.Ala846Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000395503.9",
"protein_coding": true,
"protein_id": "NP_004311.1",
"strand": true,
"transcript": "NM_004320.6",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 994,
"aa_ref": "A",
"aa_start": 846,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3493,
"cdna_start": 2720,
"cds_end": null,
"cds_length": 2985,
"cds_start": 2536,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000395503.9",
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"hgvs_c": "c.2536G>A",
"hgvs_p": "p.Ala846Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004320.6",
"protein_coding": true,
"protein_id": "ENSP00000378879.5",
"strand": true,
"transcript": "ENST00000395503.9",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1005,
"aa_ref": "A",
"aa_start": 857,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3522,
"cdna_start": 2753,
"cds_end": null,
"cds_length": 3018,
"cds_start": 2569,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000971328.1",
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"hgvs_c": "c.2569G>A",
"hgvs_p": "p.Ala857Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641387.1",
"strand": true,
"transcript": "ENST00000971328.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1001,
"aa_ref": "A",
"aa_start": 846,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3451,
"cdna_start": 2720,
"cds_end": null,
"cds_length": 3006,
"cds_start": 2536,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_173201.5",
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"hgvs_c": "c.2536G>A",
"hgvs_p": "p.Ala846Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_775293.1",
"strand": true,
"transcript": "NM_173201.5",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1001,
"aa_ref": "A",
"aa_start": 846,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3532,
"cdna_start": 2803,
"cds_end": null,
"cds_length": 3006,
"cds_start": 2536,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000357084.7",
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"hgvs_c": "c.2536G>A",
"hgvs_p": "p.Ala846Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000349595.3",
"strand": true,
"transcript": "ENST00000357084.7",
"transcript_support_level": 2
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 994,
"aa_ref": "A",
"aa_start": 846,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3487,
"cdna_start": 2720,
"cds_end": null,
"cds_length": 2985,
"cds_start": 2536,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000971325.1",
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"hgvs_c": "c.2536G>A",
"hgvs_p": "p.Ala846Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641384.1",
"strand": true,
"transcript": "ENST00000971325.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 988,
"aa_ref": "A",
"aa_start": 840,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3468,
"cdna_start": 2697,
"cds_end": null,
"cds_length": 2967,
"cds_start": 2518,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000971329.1",
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"hgvs_c": "c.2518G>A",
"hgvs_p": "p.Ala840Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641388.1",
"strand": true,
"transcript": "ENST00000971329.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 967,
"aa_ref": "A",
"aa_start": 819,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3411,
"cdna_start": 2639,
"cds_end": null,
"cds_length": 2904,
"cds_start": 2455,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000971326.1",
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"hgvs_c": "c.2455G>A",
"hgvs_p": "p.Ala819Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641385.1",
"strand": true,
"transcript": "ENST00000971326.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 961,
"aa_ref": "A",
"aa_start": 813,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3391,
"cdna_start": 2620,
"cds_end": null,
"cds_length": 2886,
"cds_start": 2437,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000971327.1",
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"hgvs_c": "c.2437G>A",
"hgvs_p": "p.Ala813Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641386.1",
"strand": true,
"transcript": "ENST00000971327.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 869,
"aa_ref": "A",
"aa_start": 721,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3142,
"cdna_start": 2369,
"cds_end": null,
"cds_length": 2610,
"cds_start": 2161,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "NM_001286075.2",
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"hgvs_c": "c.2161G>A",
"hgvs_p": "p.Ala721Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001273004.1",
"strand": true,
"transcript": "NM_001286075.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 869,
"aa_ref": "A",
"aa_start": 721,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3130,
"cdna_start": 2359,
"cds_end": null,
"cds_length": 2610,
"cds_start": 2161,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000536376.5",
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"hgvs_c": "c.2161G>A",
"hgvs_p": "p.Ala721Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000443101.1",
"strand": true,
"transcript": "ENST00000536376.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs186012808",
"effect": "missense_variant",
"frequency_reference_population": 0.000412621,
"gene_hgnc_id": 811,
"gene_symbol": "ATP2A1",
"gnomad_exomes_ac": 590,
"gnomad_exomes_af": 0.000403599,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_ac": 76,
"gnomad_genomes_af": 0.000499258,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 3,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not provided|Brody myopathy",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.794,
"pos": 28902591,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.56,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_173201.5"
}
]
}