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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: 15-25804250-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=25804250&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ATP10A",
"hgnc_id": 13542,
"hgvs_c": "c.450-23027A>T",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_024490.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.86,
"chr": "15",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.8600000143051147,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1499,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5360,
"cdna_start": null,
"cds_end": null,
"cds_length": 4500,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 21,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_024490.4",
"gene_hgnc_id": 13542,
"gene_symbol": "ATP10A",
"hgvs_c": "c.450-23027A>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000555815.7",
"protein_coding": true,
"protein_id": "NP_077816.1",
"strand": false,
"transcript": "NM_024490.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1499,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5360,
"cdna_start": null,
"cds_end": null,
"cds_length": 4500,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 21,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000555815.7",
"gene_hgnc_id": 13542,
"gene_symbol": "ATP10A",
"hgvs_c": "c.450-23027A>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_024490.4",
"protein_coding": true,
"protein_id": "ENSP00000450480.2",
"strand": false,
"transcript": "ENST00000555815.7",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1499,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6767,
"cdna_start": null,
"cds_end": null,
"cds_length": 4500,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000356865.11",
"gene_hgnc_id": 13542,
"gene_symbol": "ATP10A",
"hgvs_c": "c.450-23027A>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000349325.6",
"strand": false,
"transcript": "ENST00000356865.11",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 841,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2999,
"cdna_start": null,
"cds_end": null,
"cds_length": 2526,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 10,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000673747.1",
"gene_hgnc_id": 13542,
"gene_symbol": "ATP10A",
"hgvs_c": "c.450-23027A>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000501230.1",
"strand": false,
"transcript": "ENST00000673747.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 495,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1759,
"cdna_start": null,
"cds_end": null,
"cds_length": 1488,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000673716.1",
"gene_hgnc_id": 13542,
"gene_symbol": "ATP10A",
"hgvs_c": "c.450-23027A>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000501027.1",
"strand": false,
"transcript": "ENST00000673716.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1499,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5309,
"cdna_start": null,
"cds_end": null,
"cds_length": 4500,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_005268261.5",
"gene_hgnc_id": 13542,
"gene_symbol": "ATP10A",
"hgvs_c": "c.450-23027A>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005268318.1",
"strand": false,
"transcript": "XM_005268261.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1499,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5578,
"cdna_start": null,
"cds_end": null,
"cds_length": 4500,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011521826.3",
"gene_hgnc_id": 13542,
"gene_symbol": "ATP10A",
"hgvs_c": "c.450-23027A>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011520128.1",
"strand": false,
"transcript": "XM_011521826.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1416,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5649,
"cdna_start": null,
"cds_end": null,
"cds_length": 4251,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011521828.3",
"gene_hgnc_id": 13542,
"gene_symbol": "ATP10A",
"hgvs_c": "c.450-23027A>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011520130.1",
"strand": false,
"transcript": "XM_011521828.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1194,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5208,
"cdna_start": null,
"cds_end": null,
"cds_length": 3585,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 21,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017022437.2",
"gene_hgnc_id": 13542,
"gene_symbol": "ATP10A",
"hgvs_c": "c.-466-23027A>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016877926.1",
"strand": false,
"transcript": "XM_017022437.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1194,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4989,
"cdna_start": null,
"cds_end": null,
"cds_length": 3585,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047432890.1",
"gene_hgnc_id": 13542,
"gene_symbol": "ATP10A",
"hgvs_c": "c.-466-23027A>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047288846.1",
"strand": false,
"transcript": "XM_047432890.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1194,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4927,
"cdna_start": null,
"cds_end": null,
"cds_length": 3585,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047432891.1",
"gene_hgnc_id": 13542,
"gene_symbol": "ATP10A",
"hgvs_c": "c.-466-23027A>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047288847.1",
"strand": false,
"transcript": "XM_047432891.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 895,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000673679.1",
"gene_hgnc_id": 13542,
"gene_symbol": "ATP10A",
"hgvs_c": "n.273-23027A>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000501244.1",
"strand": false,
"transcript": "ENST00000673679.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1978,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000673898.1",
"gene_hgnc_id": 13542,
"gene_symbol": "ATP10A",
"hgvs_c": "n.750-23027A>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000673898.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 5312,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 12,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_001751368.2",
"gene_hgnc_id": 13542,
"gene_symbol": "ATP10A",
"hgvs_c": "n.681-23027A>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "XR_001751368.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs4566129",
"effect": "intron_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 13542,
"gene_symbol": "ATP10A",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.56,
"pos": 25804250,
"ref": "T",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_024490.4"
}
]
}