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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: 12-112898450-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=112898450&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 112898450,
"ref": "C",
"alt": "T",
"effect": "3_prime_UTR_variant",
"transcript": "ENST00000389385.9",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPH3A",
"gene_hgnc_id": 17056,
"hgvs_c": "n.4757C>T",
"hgvs_p": null,
"transcript": "ENST00000549913.6",
"protein_id": null,
"transcript_support_level": 1,
"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": 5188,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPH3A",
"gene_hgnc_id": 17056,
"hgvs_c": "c.*1670C>T",
"hgvs_p": null,
"transcript": "NM_001143854.2",
"protein_id": "NP_001137326.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 694,
"cds_start": -4,
"cds_end": null,
"cds_length": 2085,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4590,
"mane_select": "ENST00000389385.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPH3A",
"gene_hgnc_id": 17056,
"hgvs_c": "c.*1670C>T",
"hgvs_p": null,
"transcript": "ENST00000389385.9",
"protein_id": "ENSP00000374036.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 694,
"cds_start": -4,
"cds_end": null,
"cds_length": 2085,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4590,
"mane_select": "NM_001143854.2",
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPH3A",
"gene_hgnc_id": 17056,
"hgvs_c": "n.2262C>T",
"hgvs_p": null,
"transcript": "ENST00000549324.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 2349,
"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": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPH3A",
"gene_hgnc_id": 17056,
"hgvs_c": "n.4266C>T",
"hgvs_p": null,
"transcript": "NR_145126.2",
"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": 4697,
"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": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPH3A",
"gene_hgnc_id": 17056,
"hgvs_c": "n.4332C>T",
"hgvs_p": null,
"transcript": "NR_145127.2",
"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": 4763,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPH3A",
"gene_hgnc_id": 17056,
"hgvs_c": "c.*1670C>T",
"hgvs_p": null,
"transcript": "NM_001347952.2",
"protein_id": "NP_001334881.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 694,
"cds_start": -4,
"cds_end": null,
"cds_length": 2085,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4409,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPH3A",
"gene_hgnc_id": 17056,
"hgvs_c": "c.*1670C>T",
"hgvs_p": null,
"transcript": "NM_001347953.1",
"protein_id": "NP_001334882.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 694,
"cds_start": -4,
"cds_end": null,
"cds_length": 2085,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4398,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPH3A",
"gene_hgnc_id": 17056,
"hgvs_c": "c.*1670C>T",
"hgvs_p": null,
"transcript": "NM_001347954.2",
"protein_id": "NP_001334883.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 694,
"cds_start": -4,
"cds_end": null,
"cds_length": 2085,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4562,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPH3A",
"gene_hgnc_id": 17056,
"hgvs_c": "c.*1670C>T",
"hgvs_p": null,
"transcript": "ENST00000415485.7",
"protein_id": "ENSP00000405357.3",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 694,
"cds_start": -4,
"cds_end": null,
"cds_length": 2085,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4452,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPH3A",
"gene_hgnc_id": 17056,
"hgvs_c": "c.*1670C>T",
"hgvs_p": null,
"transcript": "NM_014954.4",
"protein_id": "NP_055769.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 690,
"cds_start": -4,
"cds_end": null,
"cds_length": 2073,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4578,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPH3A",
"gene_hgnc_id": 17056,
"hgvs_c": "c.*1670C>T",
"hgvs_p": null,
"transcript": "NM_001347955.2",
"protein_id": "NP_001334884.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 627,
"cds_start": -4,
"cds_end": null,
"cds_length": 1884,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4501,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPH3A",
"gene_hgnc_id": 17056,
"hgvs_c": "c.*1670C>T",
"hgvs_p": null,
"transcript": "XM_047428540.1",
"protein_id": "XP_047284496.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 690,
"cds_start": -4,
"cds_end": null,
"cds_length": 2073,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4386,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPH3A",
"gene_hgnc_id": 17056,
"hgvs_c": "c.*1670C>T",
"hgvs_p": null,
"transcript": "XM_017019034.3",
"protein_id": "XP_016874523.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 346,
"cds_start": -4,
"cds_end": null,
"cds_length": 1041,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5154,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RPH3A",
"gene_hgnc_id": 17056,
"dbsnp": "rs12309946",
"frequency_reference_population": 0.039759446,
"hom_count_reference_population": 141,
"allele_count_reference_population": 6056,
"gnomad_exomes_af": 0.105263,
"gnomad_genomes_af": 0.0397431,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": 6052,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 141,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9700000286102295,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.97,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.851,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000389385.9",
"gene_symbol": "RPH3A",
"hgnc_id": 17056,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.*1670C>T",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}