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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: 4-110617671-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=110617671&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 110617671,
"ref": "G",
"alt": "A",
"effect": "3_prime_UTR_variant",
"transcript": "ENST00000644743.1",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.*454C>T",
"hgvs_p": null,
"transcript": "NM_000325.6",
"protein_id": "NP_000316.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 324,
"cds_start": -4,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2294,
"mane_select": "ENST00000644743.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.*454C>T",
"hgvs_p": null,
"transcript": "ENST00000644743.1",
"protein_id": "ENSP00000495061.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 324,
"cds_start": -4,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2294,
"mane_select": "NM_000325.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.*454C>T",
"hgvs_p": null,
"transcript": "ENST00000355080.9",
"protein_id": "ENSP00000347192.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 271,
"cds_start": -4,
"cds_end": null,
"cds_length": 816,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2100,
"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": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "n.1156C>T",
"hgvs_p": null,
"transcript": "ENST00000607868.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 1398,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "n.1360C>T",
"hgvs_p": null,
"transcript": "ENST00000645131.1",
"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": 1608,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.*454C>T",
"hgvs_p": null,
"transcript": "NM_001204397.2",
"protein_id": "NP_001191326.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 317,
"cds_start": -4,
"cds_end": null,
"cds_length": 954,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2131,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.*454C>T",
"hgvs_p": null,
"transcript": "NM_001204398.1",
"protein_id": "NP_001191327.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 317,
"cds_start": -4,
"cds_end": null,
"cds_length": 954,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1871,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.*454C>T",
"hgvs_p": null,
"transcript": "NM_153426.3",
"protein_id": "NP_700475.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 317,
"cds_start": -4,
"cds_end": null,
"cds_length": 954,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1897,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.*454C>T",
"hgvs_p": null,
"transcript": "ENST00000354925.6",
"protein_id": "ENSP00000347004.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 317,
"cds_start": -4,
"cds_end": null,
"cds_length": 954,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3359,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.*454C>T",
"hgvs_p": null,
"transcript": "ENST00000394595.8",
"protein_id": "ENSP00000378095.4",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 317,
"cds_start": -4,
"cds_end": null,
"cds_length": 954,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1897,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.*454C>T",
"hgvs_p": null,
"transcript": "ENST00000614423.5",
"protein_id": "ENSP00000481951.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 290,
"cds_start": -4,
"cds_end": null,
"cds_length": 873,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1718,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.*454C>T",
"hgvs_p": null,
"transcript": "NM_001204399.1",
"protein_id": "NP_001191328.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 271,
"cds_start": -4,
"cds_end": null,
"cds_length": 816,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1733,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.*454C>T",
"hgvs_p": null,
"transcript": "NM_153427.3",
"protein_id": "NP_700476.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 271,
"cds_start": -4,
"cds_end": null,
"cds_length": 816,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1759,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.*677C>T",
"hgvs_p": null,
"transcript": "ENST00000613094.5",
"protein_id": "ENSP00000484763.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 174,
"cds_start": -4,
"cds_end": null,
"cds_length": 525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1693,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.*454C>T",
"hgvs_p": null,
"transcript": "XM_024454090.2",
"protein_id": "XP_024309858.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 206,
"cds_start": -4,
"cds_end": null,
"cds_length": 621,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1507,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"dbsnp": "rs6533526",
"frequency_reference_population": 0.040694676,
"hom_count_reference_population": 553,
"allele_count_reference_population": 7421,
"gnomad_exomes_af": 0.00453883,
"gnomad_genomes_af": 0.0478663,
"gnomad_exomes_ac": 137,
"gnomad_genomes_ac": 7284,
"gnomad_exomes_homalt": 6,
"gnomad_genomes_homalt": 547,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.3700000047683716,
"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": -0.37,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.523,
"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": -18,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -18,
"benign_score": 18,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000644743.1",
"gene_symbol": "PITX2",
"hgnc_id": 9005,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.*454C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Anterior segment dysgenesis 1,Axenfeld-Rieger syndrome type 1,Cataract,Hypoplasia of the iris,Irido-corneo-trabecular dysgenesis,PITX2-Related Eye Abnormalities,Ring dermoid of cornea,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:9",
"phenotype_combined": "not provided|Anterior segment dysgenesis 1|Hypoplasia of the iris|PITX2-Related Eye Abnormalities|Cataract|Ring dermoid of cornea|Irido-corneo-trabecular dysgenesis|Axenfeld-Rieger syndrome type 1",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}