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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: 4-110618482-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=110618482&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 110618482,
"ref": "A",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000644743.1",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.618T>G",
"hgvs_p": "p.Ser206Ser",
"transcript": "NM_000325.6",
"protein_id": "NP_000316.2",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 324,
"cds_start": 618,
"cds_end": null,
"cds_length": 975,
"cdna_start": 1235,
"cdna_end": null,
"cdna_length": 2294,
"mane_select": "ENST00000644743.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.618T>G",
"hgvs_p": "p.Ser206Ser",
"transcript": "ENST00000644743.1",
"protein_id": "ENSP00000495061.1",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 324,
"cds_start": 618,
"cds_end": null,
"cds_length": 975,
"cdna_start": 1235,
"cdna_end": null,
"cdna_length": 2294,
"mane_select": "NM_000325.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.459T>G",
"hgvs_p": "p.Ser153Ser",
"transcript": "ENST00000355080.9",
"protein_id": "ENSP00000347192.5",
"transcript_support_level": 1,
"aa_start": 153,
"aa_end": null,
"aa_length": 271,
"cds_start": 459,
"cds_end": null,
"cds_length": 816,
"cdna_start": 1041,
"cdna_end": null,
"cdna_length": 2100,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.391T>G",
"hgvs_p": "p.Tyr131Asp",
"transcript": "ENST00000613094.5",
"protein_id": "ENSP00000484763.2",
"transcript_support_level": 5,
"aa_start": 131,
"aa_end": null,
"aa_length": 174,
"cds_start": 391,
"cds_end": null,
"cds_length": 525,
"cdna_start": 647,
"cdna_end": null,
"cdna_length": 1693,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.597T>G",
"hgvs_p": "p.Ser199Ser",
"transcript": "NM_001204397.2",
"protein_id": "NP_001191326.1",
"transcript_support_level": null,
"aa_start": 199,
"aa_end": null,
"aa_length": 317,
"cds_start": 597,
"cds_end": null,
"cds_length": 954,
"cdna_start": 1072,
"cdna_end": null,
"cdna_length": 2131,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.597T>G",
"hgvs_p": "p.Ser199Ser",
"transcript": "NM_001204398.1",
"protein_id": "NP_001191327.1",
"transcript_support_level": null,
"aa_start": 199,
"aa_end": null,
"aa_length": 317,
"cds_start": 597,
"cds_end": null,
"cds_length": 954,
"cdna_start": 812,
"cdna_end": null,
"cdna_length": 1871,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.597T>G",
"hgvs_p": "p.Ser199Ser",
"transcript": "NM_153426.3",
"protein_id": "NP_700475.1",
"transcript_support_level": null,
"aa_start": 199,
"aa_end": null,
"aa_length": 317,
"cds_start": 597,
"cds_end": null,
"cds_length": 954,
"cdna_start": 838,
"cdna_end": null,
"cdna_length": 1897,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.597T>G",
"hgvs_p": "p.Ser199Ser",
"transcript": "ENST00000354925.6",
"protein_id": "ENSP00000347004.2",
"transcript_support_level": 2,
"aa_start": 199,
"aa_end": null,
"aa_length": 317,
"cds_start": 597,
"cds_end": null,
"cds_length": 954,
"cdna_start": 2303,
"cdna_end": null,
"cdna_length": 3359,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.597T>G",
"hgvs_p": "p.Ser199Ser",
"transcript": "ENST00000394595.8",
"protein_id": "ENSP00000378095.4",
"transcript_support_level": 5,
"aa_start": 199,
"aa_end": null,
"aa_length": 317,
"cds_start": 597,
"cds_end": null,
"cds_length": 954,
"cdna_start": 838,
"cdna_end": null,
"cdna_length": 1897,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.516T>G",
"hgvs_p": "p.Ser172Ser",
"transcript": "ENST00000614423.5",
"protein_id": "ENSP00000481951.2",
"transcript_support_level": 5,
"aa_start": 172,
"aa_end": null,
"aa_length": 290,
"cds_start": 516,
"cds_end": null,
"cds_length": 873,
"cdna_start": 660,
"cdna_end": null,
"cdna_length": 1718,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.597T>G",
"hgvs_p": "p.Ser199Ser",
"transcript": "ENST00000511837.5",
"protein_id": "ENSP00000421454.1",
"transcript_support_level": 5,
"aa_start": 199,
"aa_end": null,
"aa_length": 289,
"cds_start": 597,
"cds_end": null,
"cds_length": 870,
"cdna_start": 812,
"cdna_end": null,
"cdna_length": 1085,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.459T>G",
"hgvs_p": "p.Ser153Ser",
"transcript": "NM_001204399.1",
"protein_id": "NP_001191328.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 271,
"cds_start": 459,
"cds_end": null,
"cds_length": 816,
"cdna_start": 674,
"cdna_end": null,
"cdna_length": 1733,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.459T>G",
"hgvs_p": "p.Ser153Ser",
"transcript": "NM_153427.3",
"protein_id": "NP_700476.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 271,
"cds_start": 459,
"cds_end": null,
"cds_length": 816,
"cdna_start": 700,
"cdna_end": null,
"cdna_length": 1759,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.264T>G",
"hgvs_p": "p.Ser88Ser",
"transcript": "XM_024454090.2",
"protein_id": "XP_024309858.1",
"transcript_support_level": null,
"aa_start": 88,
"aa_end": null,
"aa_length": 206,
"cds_start": 264,
"cds_end": null,
"cds_length": 621,
"cdna_start": 448,
"cdna_end": null,
"cdna_length": 1507,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "n.924T>G",
"hgvs_p": null,
"transcript": "ENST00000556049.1",
"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": 941,
"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.345T>G",
"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.584T>G",
"hgvs_p": null,
"transcript": "ENST00000616641.5",
"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": 1139,
"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.588T>G",
"hgvs_p": null,
"transcript": "ENST00000644488.2",
"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": 1143,
"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.549T>G",
"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": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"hgvs_c": "c.*104T>G",
"hgvs_p": null,
"transcript": "ENST00000511990.1",
"protein_id": "ENSP00000424142.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 117,
"cds_start": -4,
"cds_end": null,
"cds_length": 355,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 463,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PITX2",
"gene_hgnc_id": 9005,
"dbsnp": "rs35946364",
"frequency_reference_population": 0.0020862687,
"hom_count_reference_population": 57,
"allele_count_reference_population": 3367,
"gnomad_exomes_af": 0.00118696,
"gnomad_genomes_af": 0.010725,
"gnomad_exomes_ac": 1735,
"gnomad_genomes_ac": 1632,
"gnomad_exomes_homalt": 22,
"gnomad_genomes_homalt": 35,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2759999930858612,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.276,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.69,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.535,
"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,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -18,
"benign_score": 18,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000644743.1",
"gene_symbol": "PITX2",
"hgnc_id": 9005,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.618T>G",
"hgvs_p": "p.Ser206Ser"
}
],
"clinvar_disease": "Anterior segment dysgenesis 1,Anterior segment dysgenesis 4,Axenfeld-Rieger syndrome type 1,Cataract,Hypoplasia of the iris,Irido-corneo-trabecular dysgenesis,PITX2-Related Eye Abnormalities,Ring dermoid of cornea,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:8",
"phenotype_combined": "not specified|Axenfeld-Rieger syndrome type 1|Cataract|PITX2-Related Eye Abnormalities|Irido-corneo-trabecular dysgenesis|Hypoplasia of the iris|Ring dermoid of cornea|Anterior segment dysgenesis 4;Axenfeld-Rieger syndrome type 1|Anterior segment dysgenesis 1|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}