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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: 15-25679947-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=25679947&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 25679947,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000555815.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10A",
"gene_hgnc_id": 13542,
"hgvs_c": "c.3894G>C",
"hgvs_p": "p.Arg1298Ser",
"transcript": "NM_024490.4",
"protein_id": "NP_077816.1",
"transcript_support_level": null,
"aa_start": 1298,
"aa_end": null,
"aa_length": 1499,
"cds_start": 3894,
"cds_end": null,
"cds_length": 4500,
"cdna_start": 4125,
"cdna_end": null,
"cdna_length": 5360,
"mane_select": "ENST00000555815.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10A",
"gene_hgnc_id": 13542,
"hgvs_c": "c.3894G>C",
"hgvs_p": "p.Arg1298Ser",
"transcript": "ENST00000555815.7",
"protein_id": "ENSP00000450480.2",
"transcript_support_level": 5,
"aa_start": 1298,
"aa_end": null,
"aa_length": 1499,
"cds_start": 3894,
"cds_end": null,
"cds_length": 4500,
"cdna_start": 4125,
"cdna_end": null,
"cdna_length": 5360,
"mane_select": "NM_024490.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10A",
"gene_hgnc_id": 13542,
"hgvs_c": "c.3894G>C",
"hgvs_p": "p.Arg1298Ser",
"transcript": "ENST00000356865.11",
"protein_id": "ENSP00000349325.6",
"transcript_support_level": 1,
"aa_start": 1298,
"aa_end": null,
"aa_length": 1499,
"cds_start": 3894,
"cds_end": null,
"cds_length": 4500,
"cdna_start": 4093,
"cdna_end": null,
"cdna_length": 6767,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10A",
"gene_hgnc_id": 13542,
"hgvs_c": "c.3894G>C",
"hgvs_p": "p.Arg1298Ser",
"transcript": "XM_005268261.5",
"protein_id": "XP_005268318.1",
"transcript_support_level": null,
"aa_start": 1298,
"aa_end": null,
"aa_length": 1499,
"cds_start": 3894,
"cds_end": null,
"cds_length": 4500,
"cdna_start": 4074,
"cdna_end": null,
"cdna_length": 5309,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10A",
"gene_hgnc_id": 13542,
"hgvs_c": "c.3894G>C",
"hgvs_p": "p.Arg1298Ser",
"transcript": "XM_011521826.3",
"protein_id": "XP_011520128.1",
"transcript_support_level": null,
"aa_start": 1298,
"aa_end": null,
"aa_length": 1499,
"cds_start": 3894,
"cds_end": null,
"cds_length": 4500,
"cdna_start": 4343,
"cdna_end": null,
"cdna_length": 5578,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10A",
"gene_hgnc_id": 13542,
"hgvs_c": "c.3894G>C",
"hgvs_p": "p.Arg1298Ser",
"transcript": "XM_011521828.3",
"protein_id": "XP_011520130.1",
"transcript_support_level": null,
"aa_start": 1298,
"aa_end": null,
"aa_length": 1416,
"cds_start": 3894,
"cds_end": null,
"cds_length": 4251,
"cdna_start": 4125,
"cdna_end": null,
"cdna_length": 5649,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10A",
"gene_hgnc_id": 13542,
"hgvs_c": "c.2979G>C",
"hgvs_p": "p.Arg993Ser",
"transcript": "XM_011521829.3",
"protein_id": "XP_011520131.1",
"transcript_support_level": null,
"aa_start": 993,
"aa_end": null,
"aa_length": 1194,
"cds_start": 2979,
"cds_end": null,
"cds_length": 3585,
"cdna_start": 3133,
"cdna_end": null,
"cdna_length": 4368,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10A",
"gene_hgnc_id": 13542,
"hgvs_c": "c.2979G>C",
"hgvs_p": "p.Arg993Ser",
"transcript": "XM_017022437.2",
"protein_id": "XP_016877926.1",
"transcript_support_level": null,
"aa_start": 993,
"aa_end": null,
"aa_length": 1194,
"cds_start": 2979,
"cds_end": null,
"cds_length": 3585,
"cdna_start": 3973,
"cdna_end": null,
"cdna_length": 5208,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10A",
"gene_hgnc_id": 13542,
"hgvs_c": "c.2979G>C",
"hgvs_p": "p.Arg993Ser",
"transcript": "XM_047432890.1",
"protein_id": "XP_047288846.1",
"transcript_support_level": null,
"aa_start": 993,
"aa_end": null,
"aa_length": 1194,
"cds_start": 2979,
"cds_end": null,
"cds_length": 3585,
"cdna_start": 3754,
"cdna_end": null,
"cdna_length": 4989,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10A",
"gene_hgnc_id": 13542,
"hgvs_c": "c.2979G>C",
"hgvs_p": "p.Arg993Ser",
"transcript": "XM_047432891.1",
"protein_id": "XP_047288847.1",
"transcript_support_level": null,
"aa_start": 993,
"aa_end": null,
"aa_length": 1194,
"cds_start": 2979,
"cds_end": null,
"cds_length": 3585,
"cdna_start": 3692,
"cdna_end": null,
"cdna_length": 4927,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10A",
"gene_hgnc_id": 13542,
"hgvs_c": "c.2979G>C",
"hgvs_p": "p.Arg993Ser",
"transcript": "XM_047432892.1",
"protein_id": "XP_047288848.1",
"transcript_support_level": null,
"aa_start": 993,
"aa_end": null,
"aa_length": 1194,
"cds_start": 2979,
"cds_end": null,
"cds_length": 3585,
"cdna_start": 3097,
"cdna_end": null,
"cdna_length": 4332,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10A",
"gene_hgnc_id": 13542,
"hgvs_c": "n.1686G>C",
"hgvs_p": null,
"transcript": "ENST00000555450.2",
"protein_id": null,
"transcript_support_level": 3,
"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": 2254,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10A",
"gene_hgnc_id": 13542,
"hgvs_c": "n.4556G>C",
"hgvs_p": null,
"transcript": "ENST00000673680.1",
"protein_id": null,
"transcript_support_level": null,
"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": 5380,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10A",
"gene_hgnc_id": 13542,
"hgvs_c": "n.3239G>C",
"hgvs_p": null,
"transcript": "ENST00000673805.1",
"protein_id": null,
"transcript_support_level": null,
"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": 4450,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10A",
"gene_hgnc_id": 13542,
"hgvs_c": "n.2221G>C",
"hgvs_p": null,
"transcript": "ENST00000674021.1",
"protein_id": null,
"transcript_support_level": null,
"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": 3265,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10A",
"gene_hgnc_id": 13542,
"hgvs_c": "n.*182G>C",
"hgvs_p": null,
"transcript": "ENST00000674138.1",
"protein_id": null,
"transcript_support_level": null,
"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": 807,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATP10A",
"gene_hgnc_id": 13542,
"dbsnp": "rs3816800",
"frequency_reference_population": 0.46892747,
"hom_count_reference_population": 177960,
"allele_count_reference_population": 751204,
"gnomad_exomes_af": 0.468481,
"gnomad_genomes_af": 0.47319,
"gnomad_exomes_ac": 679264,
"gnomad_genomes_ac": 71940,
"gnomad_exomes_homalt": 160695,
"gnomad_genomes_homalt": 17265,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.00003221201404812746,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.1599999964237213,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.038,
"revel_prediction": "Benign",
"alphamissense_score": 0.0765,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.69,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.289,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.16,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BA1",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000555815.7",
"gene_symbol": "ATP10A",
"hgnc_id": 13542,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3894G>C",
"hgvs_p": "p.Arg1298Ser"
}
],
"clinvar_disease": "ATP10A-related disorder",
"clinvar_classification": "Benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "ATP10A-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}