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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: 12-26400213-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=26400213&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 26400213,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_002223.4",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 53,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR2",
"gene_hgnc_id": 6181,
"hgvs_c": "c.7445T>C",
"hgvs_p": "p.Leu2482Pro",
"transcript": "NM_002223.4",
"protein_id": "NP_002214.2",
"transcript_support_level": null,
"aa_start": 2482,
"aa_end": null,
"aa_length": 2701,
"cds_start": 7445,
"cds_end": null,
"cds_length": 8106,
"cdna_start": 7858,
"cdna_end": null,
"cdna_length": 12564,
"mane_select": "ENST00000381340.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 53,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR2",
"gene_hgnc_id": 6181,
"hgvs_c": "c.7445T>C",
"hgvs_p": "p.Leu2482Pro",
"transcript": "ENST00000381340.8",
"protein_id": "ENSP00000370744.3",
"transcript_support_level": 1,
"aa_start": 2482,
"aa_end": null,
"aa_length": 2701,
"cds_start": 7445,
"cds_end": null,
"cds_length": 8106,
"cdna_start": 7858,
"cdna_end": null,
"cdna_length": 12564,
"mane_select": "NM_002223.4",
"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": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR2",
"gene_hgnc_id": 6181,
"hgvs_c": "n.*1964T>C",
"hgvs_p": null,
"transcript": "ENST00000451599.6",
"protein_id": "ENSP00000408287.2",
"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": 2577,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR2",
"gene_hgnc_id": 6181,
"hgvs_c": "n.*1964T>C",
"hgvs_p": null,
"transcript": "ENST00000451599.6",
"protein_id": "ENSP00000408287.2",
"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": 2577,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 53,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR2",
"gene_hgnc_id": 6181,
"hgvs_c": "c.7442T>C",
"hgvs_p": "p.Leu2481Pro",
"transcript": "NM_001414174.1",
"protein_id": "NP_001401103.1",
"transcript_support_level": null,
"aa_start": 2481,
"aa_end": null,
"aa_length": 2700,
"cds_start": 7442,
"cds_end": null,
"cds_length": 8103,
"cdna_start": 7855,
"cdna_end": null,
"cdna_length": 12561,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 51,
"exon_rank_end": null,
"exon_count": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR2",
"gene_hgnc_id": 6181,
"hgvs_c": "c.7226T>C",
"hgvs_p": "p.Leu2409Pro",
"transcript": "NM_001414175.1",
"protein_id": "NP_001401104.1",
"transcript_support_level": null,
"aa_start": 2409,
"aa_end": null,
"aa_length": 2628,
"cds_start": 7226,
"cds_end": null,
"cds_length": 7887,
"cdna_start": 7639,
"cdna_end": null,
"cdna_length": 12345,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 54,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR2",
"gene_hgnc_id": 6181,
"hgvs_c": "c.7505T>C",
"hgvs_p": "p.Leu2502Pro",
"transcript": "XM_017019266.2",
"protein_id": "XP_016874755.1",
"transcript_support_level": null,
"aa_start": 2502,
"aa_end": null,
"aa_length": 2721,
"cds_start": 7505,
"cds_end": null,
"cds_length": 8166,
"cdna_start": 7918,
"cdna_end": null,
"cdna_length": 12624,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 55,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR2",
"gene_hgnc_id": 6181,
"hgvs_c": "c.7439T>C",
"hgvs_p": "p.Leu2480Pro",
"transcript": "XM_047428801.1",
"protein_id": "XP_047284757.1",
"transcript_support_level": null,
"aa_start": 2480,
"aa_end": null,
"aa_length": 2699,
"cds_start": 7439,
"cds_end": null,
"cds_length": 8100,
"cdna_start": 7980,
"cdna_end": null,
"cdna_length": 12686,
"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": 55,
"exon_rank_end": null,
"exon_count": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR2",
"gene_hgnc_id": 6181,
"hgvs_c": "n.8099T>C",
"hgvs_p": null,
"transcript": "XR_001748686.3",
"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": 8127,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000255968",
"gene_hgnc_id": 58268,
"hgvs_c": "n.53-444A>G",
"hgvs_p": null,
"transcript": "ENST00000535324.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 775,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ITPR2-AS2",
"gene_hgnc_id": 58268,
"hgvs_c": "n.82-444A>G",
"hgvs_p": null,
"transcript": "NR_199072.1",
"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": 2146,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ITPR2",
"gene_hgnc_id": 6181,
"dbsnp": "rs368549044",
"frequency_reference_population": 0.00000996645,
"hom_count_reference_population": 0,
"allele_count_reference_population": 16,
"gnomad_exomes_af": 0.00000963391,
"gnomad_genomes_af": 0.0000131418,
"gnomad_exomes_ac": 14,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9662054777145386,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.953,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9916,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.59,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.782,
"phylop100way_prediction": "Pathogenic",
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_002223.4",
"gene_symbol": "ITPR2",
"hgnc_id": 6181,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.7445T>C",
"hgvs_p": "p.Leu2482Pro"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000535324.1",
"gene_symbol": "ENSG00000255968",
"hgnc_id": 58268,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.53-444A>G",
"hgvs_p": null
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NR_199072.1",
"gene_symbol": "ITPR2-AS2",
"hgnc_id": 58268,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.82-444A>G",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}