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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: 1-1522810-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=1522810&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 1522810,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000378756.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATAD3A",
"gene_hgnc_id": 25567,
"hgvs_c": "c.817C>A",
"hgvs_p": "p.Arg273Ser",
"transcript": "NM_001170535.3",
"protein_id": "NP_001164006.1",
"transcript_support_level": null,
"aa_start": 273,
"aa_end": null,
"aa_length": 586,
"cds_start": 817,
"cds_end": null,
"cds_length": 1761,
"cdna_start": 924,
"cdna_end": null,
"cdna_length": 2481,
"mane_select": "ENST00000378756.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATAD3A",
"gene_hgnc_id": 25567,
"hgvs_c": "c.817C>A",
"hgvs_p": "p.Arg273Ser",
"transcript": "ENST00000378756.8",
"protein_id": "ENSP00000368031.3",
"transcript_support_level": 1,
"aa_start": 273,
"aa_end": null,
"aa_length": 586,
"cds_start": 817,
"cds_end": null,
"cds_length": 1761,
"cdna_start": 924,
"cdna_end": null,
"cdna_length": 2481,
"mane_select": "NM_001170535.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATAD3A",
"gene_hgnc_id": 25567,
"hgvs_c": "c.961C>A",
"hgvs_p": "p.Arg321Ser",
"transcript": "NM_018188.5",
"protein_id": "NP_060658.3",
"transcript_support_level": null,
"aa_start": 321,
"aa_end": null,
"aa_length": 634,
"cds_start": 961,
"cds_end": null,
"cds_length": 1905,
"cdna_start": 1068,
"cdna_end": null,
"cdna_length": 2625,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATAD3A",
"gene_hgnc_id": 25567,
"hgvs_c": "c.961C>A",
"hgvs_p": "p.Arg321Ser",
"transcript": "ENST00000378755.9",
"protein_id": "ENSP00000368030.5",
"transcript_support_level": 2,
"aa_start": 321,
"aa_end": null,
"aa_length": 634,
"cds_start": 961,
"cds_end": null,
"cds_length": 1905,
"cdna_start": 1055,
"cdna_end": null,
"cdna_length": 2612,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATAD3A",
"gene_hgnc_id": 25567,
"hgvs_c": "c.580C>A",
"hgvs_p": "p.Arg194Ser",
"transcript": "NM_001170536.3",
"protein_id": "NP_001164007.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 507,
"cds_start": 580,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 773,
"cdna_end": null,
"cdna_length": 2330,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATAD3A",
"gene_hgnc_id": 25567,
"hgvs_c": "c.580C>A",
"hgvs_p": "p.Arg194Ser",
"transcript": "ENST00000536055.6",
"protein_id": "ENSP00000439290.1",
"transcript_support_level": 2,
"aa_start": 194,
"aa_end": null,
"aa_length": 507,
"cds_start": 580,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 773,
"cdna_end": null,
"cdna_length": 2330,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATAD3A",
"gene_hgnc_id": 25567,
"hgvs_c": "c.655C>A",
"hgvs_p": "p.Arg219Ser",
"transcript": "XM_047424288.1",
"protein_id": "XP_047280244.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 532,
"cds_start": 655,
"cds_end": null,
"cds_length": 1599,
"cdna_start": 1149,
"cdna_end": null,
"cdna_length": 2706,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATAD3A",
"gene_hgnc_id": 25567,
"hgvs_c": "c.817C>A",
"hgvs_p": "p.Arg273Ser",
"transcript": "XM_047424289.1",
"protein_id": "XP_047280245.1",
"transcript_support_level": null,
"aa_start": 273,
"aa_end": null,
"aa_length": 491,
"cds_start": 817,
"cds_end": null,
"cds_length": 1476,
"cdna_start": 924,
"cdna_end": null,
"cdna_length": 1637,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATAD3A",
"gene_hgnc_id": 25567,
"hgvs_c": "c.817C>A",
"hgvs_p": "p.Arg273Ser",
"transcript": "XM_047424290.1",
"protein_id": "XP_047280246.1",
"transcript_support_level": null,
"aa_start": 273,
"aa_end": null,
"aa_length": 483,
"cds_start": 817,
"cds_end": null,
"cds_length": 1452,
"cdna_start": 924,
"cdna_end": null,
"cdna_length": 1966,
"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": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATAD3A",
"gene_hgnc_id": 25567,
"hgvs_c": "n.*363C>A",
"hgvs_p": null,
"transcript": "ENST00000339113.9",
"protein_id": "ENSP00000339421.5",
"transcript_support_level": 2,
"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": 2266,
"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": 6,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATAD3A",
"gene_hgnc_id": 25567,
"hgvs_c": "n.1154C>A",
"hgvs_p": null,
"transcript": "ENST00000672388.1",
"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": 2610,
"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": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATAD3A",
"gene_hgnc_id": 25567,
"hgvs_c": "n.*363C>A",
"hgvs_p": null,
"transcript": "ENST00000339113.9",
"protein_id": "ENSP00000339421.5",
"transcript_support_level": 2,
"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": 2266,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATAD3A",
"gene_hgnc_id": 25567,
"hgvs_c": "n.*30C>A",
"hgvs_p": null,
"transcript": "ENST00000429957.1",
"protein_id": null,
"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": 498,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATAD3A",
"gene_hgnc_id": 25567,
"dbsnp": "rs574343682",
"frequency_reference_population": 0.0000049654714,
"hom_count_reference_population": 0,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.00000479541,
"gnomad_genomes_af": 0.00000660519,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8835234045982361,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.2800000011920929,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.734,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.5311,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.37,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.305,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.28,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000378756.8",
"gene_symbol": "ATAD3A",
"hgnc_id": 25567,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR,SD",
"hgvs_c": "c.817C>A",
"hgvs_p": "p.Arg273Ser"
}
],
"clinvar_disease": "Harel-Yoon syndrome,Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Harel-Yoon syndrome|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}