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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: 2-70275150-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=70275150&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 70275150,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_016297.4",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYOX1",
"gene_hgnc_id": 20588,
"hgvs_c": "c.686C>T",
"hgvs_p": "p.Thr229Met",
"transcript": "NM_016297.4",
"protein_id": "NP_057381.3",
"transcript_support_level": null,
"aa_start": 229,
"aa_end": null,
"aa_length": 505,
"cds_start": 686,
"cds_end": null,
"cds_length": 1518,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000433351.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_016297.4"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYOX1",
"gene_hgnc_id": 20588,
"hgvs_c": "c.686C>T",
"hgvs_p": "p.Thr229Met",
"transcript": "ENST00000433351.7",
"protein_id": "ENSP00000387654.2",
"transcript_support_level": 1,
"aa_start": 229,
"aa_end": null,
"aa_length": 505,
"cds_start": 686,
"cds_end": null,
"cds_length": 1518,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_016297.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000433351.7"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYOX1",
"gene_hgnc_id": 20588,
"hgvs_c": "c.797C>T",
"hgvs_p": "p.Thr266Met",
"transcript": "ENST00000884434.1",
"protein_id": "ENSP00000554493.1",
"transcript_support_level": null,
"aa_start": 266,
"aa_end": null,
"aa_length": 542,
"cds_start": 797,
"cds_end": null,
"cds_length": 1629,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884434.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYOX1",
"gene_hgnc_id": 20588,
"hgvs_c": "c.686C>T",
"hgvs_p": "p.Thr229Met",
"transcript": "ENST00000955833.1",
"protein_id": "ENSP00000625892.1",
"transcript_support_level": null,
"aa_start": 229,
"aa_end": null,
"aa_length": 490,
"cds_start": 686,
"cds_end": null,
"cds_length": 1473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955833.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYOX1",
"gene_hgnc_id": 20588,
"hgvs_c": "c.632C>T",
"hgvs_p": "p.Thr211Met",
"transcript": "ENST00000923107.1",
"protein_id": "ENSP00000593166.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 487,
"cds_start": 632,
"cds_end": null,
"cds_length": 1464,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923107.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYOX1",
"gene_hgnc_id": 20588,
"hgvs_c": "c.686C>T",
"hgvs_p": "p.Thr229Met",
"transcript": "ENST00000955832.1",
"protein_id": "ENSP00000625891.1",
"transcript_support_level": null,
"aa_start": 229,
"aa_end": null,
"aa_length": 454,
"cds_start": 686,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955832.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYOX1",
"gene_hgnc_id": 20588,
"hgvs_c": "c.686C>T",
"hgvs_p": "p.Thr229Met",
"transcript": "ENST00000264441.9",
"protein_id": "ENSP00000264441.5",
"transcript_support_level": 5,
"aa_start": 229,
"aa_end": null,
"aa_length": 293,
"cds_start": 686,
"cds_end": null,
"cds_length": 882,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264441.9"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYOX1",
"gene_hgnc_id": 20588,
"hgvs_c": "c.455C>T",
"hgvs_p": "p.Thr152Met",
"transcript": "ENST00000414812.5",
"protein_id": "ENSP00000413178.1",
"transcript_support_level": 3,
"aa_start": 152,
"aa_end": null,
"aa_length": 208,
"cds_start": 455,
"cds_end": null,
"cds_length": 628,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000414812.5"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYOX1",
"gene_hgnc_id": 20588,
"hgvs_c": "c.455C>T",
"hgvs_p": "p.Thr152Met",
"transcript": "ENST00000451279.1",
"protein_id": "ENSP00000408751.1",
"transcript_support_level": 4,
"aa_start": 152,
"aa_end": null,
"aa_length": 153,
"cds_start": 455,
"cds_end": null,
"cds_length": 463,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000451279.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYOX1",
"gene_hgnc_id": 20588,
"hgvs_c": "c.455C>T",
"hgvs_p": "p.Thr152Met",
"transcript": "XM_047444689.1",
"protein_id": "XP_047300645.1",
"transcript_support_level": null,
"aa_start": 152,
"aa_end": null,
"aa_length": 428,
"cds_start": 455,
"cds_end": null,
"cds_length": 1287,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047444689.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYOX1",
"gene_hgnc_id": 20588,
"hgvs_c": "n.393C>T",
"hgvs_p": null,
"transcript": "ENST00000480949.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000480949.1"
},
{
"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": "PCYOX1",
"gene_hgnc_id": 20588,
"hgvs_c": "c.*66C>T",
"hgvs_p": null,
"transcript": "ENST00000422380.5",
"protein_id": "ENSP00000404327.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 128,
"cds_start": null,
"cds_end": null,
"cds_length": 389,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000422380.5"
}
],
"gene_symbol": "PCYOX1",
"gene_hgnc_id": 20588,
"dbsnp": "rs199918295",
"frequency_reference_population": 0.000095440424,
"hom_count_reference_population": 2,
"allele_count_reference_population": 154,
"gnomad_exomes_af": 0.0000958062,
"gnomad_genomes_af": 0.0000919311,
"gnomad_exomes_ac": 140,
"gnomad_genomes_ac": 14,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.011731177568435669,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.041,
"revel_prediction": "Benign",
"alphamissense_score": 0.065,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.55,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.36,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_016297.4",
"gene_symbol": "PCYOX1",
"hgnc_id": 20588,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.686C>T",
"hgvs_p": "p.Thr229Met"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}