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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: X-47202951-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=47202951&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 47202951,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000335972.11",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA1",
"gene_hgnc_id": 12469,
"hgvs_c": "c.1242C>T",
"hgvs_p": "p.Ser414Ser",
"transcript": "NM_003334.4",
"protein_id": "NP_003325.2",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 1058,
"cds_start": 1242,
"cds_end": null,
"cds_length": 3177,
"cdna_start": 1438,
"cdna_end": null,
"cdna_length": 3572,
"mane_select": "ENST00000335972.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA1",
"gene_hgnc_id": 12469,
"hgvs_c": "c.1242C>T",
"hgvs_p": "p.Ser414Ser",
"transcript": "ENST00000335972.11",
"protein_id": "ENSP00000338413.6",
"transcript_support_level": 1,
"aa_start": 414,
"aa_end": null,
"aa_length": 1058,
"cds_start": 1242,
"cds_end": null,
"cds_length": 3177,
"cdna_start": 1438,
"cdna_end": null,
"cdna_length": 3572,
"mane_select": "NM_003334.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA1",
"gene_hgnc_id": 12469,
"hgvs_c": "c.1242C>T",
"hgvs_p": "p.Ser414Ser",
"transcript": "ENST00000377351.8",
"protein_id": "ENSP00000366568.4",
"transcript_support_level": 1,
"aa_start": 414,
"aa_end": null,
"aa_length": 1058,
"cds_start": 1242,
"cds_end": null,
"cds_length": 3177,
"cdna_start": 1332,
"cdna_end": null,
"cdna_length": 3466,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA1",
"gene_hgnc_id": 12469,
"hgvs_c": "c.1284C>T",
"hgvs_p": "p.Ser428Ser",
"transcript": "NM_001440807.1",
"protein_id": "NP_001427736.1",
"transcript_support_level": null,
"aa_start": 428,
"aa_end": null,
"aa_length": 1072,
"cds_start": 1284,
"cds_end": null,
"cds_length": 3219,
"cdna_start": 1485,
"cdna_end": null,
"cdna_length": 3619,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA1",
"gene_hgnc_id": 12469,
"hgvs_c": "c.1260C>T",
"hgvs_p": "p.Ser420Ser",
"transcript": "NM_001440809.1",
"protein_id": "NP_001427738.1",
"transcript_support_level": null,
"aa_start": 420,
"aa_end": null,
"aa_length": 1064,
"cds_start": 1260,
"cds_end": null,
"cds_length": 3195,
"cdna_start": 1516,
"cdna_end": null,
"cdna_length": 3650,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA1",
"gene_hgnc_id": 12469,
"hgvs_c": "c.1260C>T",
"hgvs_p": "p.Ser420Ser",
"transcript": "NM_001440810.1",
"protein_id": "NP_001427739.1",
"transcript_support_level": null,
"aa_start": 420,
"aa_end": null,
"aa_length": 1064,
"cds_start": 1260,
"cds_end": null,
"cds_length": 3195,
"cdna_start": 1513,
"cdna_end": null,
"cdna_length": 3647,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA1",
"gene_hgnc_id": 12469,
"hgvs_c": "c.1242C>T",
"hgvs_p": "p.Ser414Ser",
"transcript": "NM_001440811.1",
"protein_id": "NP_001427740.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 1058,
"cds_start": 1242,
"cds_end": null,
"cds_length": 3177,
"cdna_start": 1552,
"cdna_end": null,
"cdna_length": 3686,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA1",
"gene_hgnc_id": 12469,
"hgvs_c": "c.1242C>T",
"hgvs_p": "p.Ser414Ser",
"transcript": "NM_001440812.1",
"protein_id": "NP_001427741.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 1058,
"cds_start": 1242,
"cds_end": null,
"cds_length": 3177,
"cdna_start": 1511,
"cdna_end": null,
"cdna_length": 3645,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA1",
"gene_hgnc_id": 12469,
"hgvs_c": "c.1242C>T",
"hgvs_p": "p.Ser414Ser",
"transcript": "NM_153280.3",
"protein_id": "NP_695012.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 1058,
"cds_start": 1242,
"cds_end": null,
"cds_length": 3177,
"cdna_start": 1346,
"cdna_end": null,
"cdna_length": 3480,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA1",
"gene_hgnc_id": 12469,
"hgvs_c": "c.1395C>T",
"hgvs_p": "p.Ser465Ser",
"transcript": "XM_017029777.2",
"protein_id": "XP_016885266.1",
"transcript_support_level": null,
"aa_start": 465,
"aa_end": null,
"aa_length": 1109,
"cds_start": 1395,
"cds_end": null,
"cds_length": 3330,
"cdna_start": 5769,
"cdna_end": null,
"cdna_length": 7903,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA1",
"gene_hgnc_id": 12469,
"hgvs_c": "c.1395C>T",
"hgvs_p": "p.Ser465Ser",
"transcript": "XM_047442420.1",
"protein_id": "XP_047298376.1",
"transcript_support_level": null,
"aa_start": 465,
"aa_end": null,
"aa_length": 1109,
"cds_start": 1395,
"cds_end": null,
"cds_length": 3330,
"cdna_start": 2847,
"cdna_end": null,
"cdna_length": 4981,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA1",
"gene_hgnc_id": 12469,
"hgvs_c": "c.1326C>T",
"hgvs_p": "p.Ser442Ser",
"transcript": "XM_017029778.3",
"protein_id": "XP_016885267.1",
"transcript_support_level": null,
"aa_start": 442,
"aa_end": null,
"aa_length": 1086,
"cds_start": 1326,
"cds_end": null,
"cds_length": 3261,
"cdna_start": 3734,
"cdna_end": null,
"cdna_length": 5868,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA1",
"gene_hgnc_id": 12469,
"hgvs_c": "c.1323C>T",
"hgvs_p": "p.Ser441Ser",
"transcript": "XM_047442421.1",
"protein_id": "XP_047298377.1",
"transcript_support_level": null,
"aa_start": 441,
"aa_end": null,
"aa_length": 1085,
"cds_start": 1323,
"cds_end": null,
"cds_length": 3258,
"cdna_start": 1563,
"cdna_end": null,
"cdna_length": 3697,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA1",
"gene_hgnc_id": 12469,
"hgvs_c": "c.1323C>T",
"hgvs_p": "p.Ser441Ser",
"transcript": "XM_047442422.1",
"protein_id": "XP_047298378.1",
"transcript_support_level": null,
"aa_start": 441,
"aa_end": null,
"aa_length": 1085,
"cds_start": 1323,
"cds_end": null,
"cds_length": 3258,
"cdna_start": 1560,
"cdna_end": null,
"cdna_length": 3694,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA1",
"gene_hgnc_id": 12469,
"hgvs_c": "c.1242C>T",
"hgvs_p": "p.Ser414Ser",
"transcript": "XM_017029780.2",
"protein_id": "XP_016885269.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 1058,
"cds_start": 1242,
"cds_end": null,
"cds_length": 3177,
"cdna_start": 3687,
"cdna_end": null,
"cdna_length": 5821,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA1",
"gene_hgnc_id": 12469,
"hgvs_c": "c.1242C>T",
"hgvs_p": "p.Ser414Ser",
"transcript": "XM_047442424.1",
"protein_id": "XP_047298380.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 1058,
"cds_start": 1242,
"cds_end": null,
"cds_length": 3177,
"cdna_start": 1308,
"cdna_end": null,
"cdna_length": 3442,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA1",
"gene_hgnc_id": 12469,
"hgvs_c": "c.1242C>T",
"hgvs_p": "p.Ser414Ser",
"transcript": "XM_047442425.1",
"protein_id": "XP_047298381.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 1058,
"cds_start": 1242,
"cds_end": null,
"cds_length": 3177,
"cdna_start": 1289,
"cdna_end": null,
"cdna_length": 3423,
"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": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBA1",
"gene_hgnc_id": 12469,
"hgvs_c": "n.131C>T",
"hgvs_p": null,
"transcript": "ENST00000490869.1",
"protein_id": null,
"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": 917,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "UBA1",
"gene_hgnc_id": 12469,
"dbsnp": "rs369843264",
"frequency_reference_population": 0.00033571225,
"hom_count_reference_population": 136,
"allele_count_reference_population": 406,
"gnomad_exomes_af": 0.000337074,
"gnomad_genomes_af": 0.000322332,
"gnomad_exomes_ac": 370,
"gnomad_genomes_ac": 36,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6499999761581421,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"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": -0.65,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.486,
"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": -17,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS2",
"acmg_by_gene": [
{
"score": -17,
"benign_score": 17,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000335972.11",
"gene_symbol": "UBA1",
"hgnc_id": 12469,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL,Unknown",
"hgvs_c": "c.1242C>T",
"hgvs_p": "p.Ser414Ser"
}
],
"clinvar_disease": "Inborn genetic diseases,Infantile-onset X-linked spinal muscular atrophy,UBA1-related disorder,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4 B:2",
"phenotype_combined": "Infantile-onset X-linked spinal muscular atrophy|Inborn genetic diseases|UBA1-related disorder|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}