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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: 3-4683761-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=4683761&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 4683761,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_001378452.1",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3461A>G",
"hgvs_p": "p.Asp1154Gly",
"transcript": "NM_001378452.1",
"protein_id": "NP_001365381.1",
"transcript_support_level": null,
"aa_start": 1154,
"aa_end": null,
"aa_length": 2758,
"cds_start": 3461,
"cds_end": null,
"cds_length": 8277,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000649015.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001378452.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3461A>G",
"hgvs_p": "p.Asp1154Gly",
"transcript": "ENST00000649015.2",
"protein_id": "ENSP00000497605.1",
"transcript_support_level": null,
"aa_start": 1154,
"aa_end": null,
"aa_length": 2758,
"cds_start": 3461,
"cds_end": null,
"cds_length": 8277,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001378452.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000649015.2"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3434A>G",
"hgvs_p": "p.Asp1145Gly",
"transcript": "ENST00000354582.12",
"protein_id": "ENSP00000346595.8",
"transcript_support_level": 5,
"aa_start": 1145,
"aa_end": null,
"aa_length": 2750,
"cds_start": 3434,
"cds_end": null,
"cds_length": 8253,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000354582.12"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3434A>G",
"hgvs_p": "p.Asp1145Gly",
"transcript": "ENST00000648266.1",
"protein_id": "ENSP00000498014.1",
"transcript_support_level": null,
"aa_start": 1145,
"aa_end": null,
"aa_length": 2749,
"cds_start": 3434,
"cds_end": null,
"cds_length": 8250,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000648266.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3416A>G",
"hgvs_p": "p.Asp1139Gly",
"transcript": "ENST00000650294.1",
"protein_id": "ENSP00000498056.1",
"transcript_support_level": null,
"aa_start": 1139,
"aa_end": null,
"aa_length": 2744,
"cds_start": 3416,
"cds_end": null,
"cds_length": 8235,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000650294.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3416A>G",
"hgvs_p": "p.Asp1139Gly",
"transcript": "ENST00000443694.5",
"protein_id": "ENSP00000401671.2",
"transcript_support_level": 1,
"aa_start": 1139,
"aa_end": null,
"aa_length": 2743,
"cds_start": 3416,
"cds_end": null,
"cds_length": 8232,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000443694.5"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3389A>G",
"hgvs_p": "p.Asp1130Gly",
"transcript": "ENST00000648309.1",
"protein_id": "ENSP00000497026.1",
"transcript_support_level": null,
"aa_start": 1130,
"aa_end": null,
"aa_length": 2734,
"cds_start": 3389,
"cds_end": null,
"cds_length": 8205,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000648309.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3434A>G",
"hgvs_p": "p.Asp1145Gly",
"transcript": "ENST00000357086.10",
"protein_id": "ENSP00000349597.4",
"transcript_support_level": 1,
"aa_start": 1145,
"aa_end": null,
"aa_length": 2710,
"cds_start": 3434,
"cds_end": null,
"cds_length": 8133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000357086.10"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3389A>G",
"hgvs_p": "p.Asp1130Gly",
"transcript": "ENST00000456211.8",
"protein_id": "ENSP00000397885.2",
"transcript_support_level": 1,
"aa_start": 1130,
"aa_end": null,
"aa_length": 2695,
"cds_start": 3389,
"cds_end": null,
"cds_length": 8088,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000456211.8"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.1271A>G",
"hgvs_p": "p.Asp424Gly",
"transcript": "ENST00000648038.1",
"protein_id": "ENSP00000497872.1",
"transcript_support_level": null,
"aa_start": 424,
"aa_end": null,
"aa_length": 2012,
"cds_start": 1271,
"cds_end": null,
"cds_length": 6039,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000648038.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.761A>G",
"hgvs_p": "p.Asp254Gly",
"transcript": "ENST00000648431.1",
"protein_id": "ENSP00000498149.1",
"transcript_support_level": null,
"aa_start": 254,
"aa_end": null,
"aa_length": 1817,
"cds_start": 761,
"cds_end": null,
"cds_length": 5454,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000648431.1"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.368A>G",
"hgvs_p": "p.Asp123Gly",
"transcript": "ENST00000648212.1",
"protein_id": "ENSP00000498022.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 1738,
"cds_start": 368,
"cds_end": null,
"cds_length": 5217,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000648212.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.996+29875A>G",
"hgvs_p": null,
"transcript": "ENST00000544951.6",
"protein_id": "ENSP00000440564.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 721,
"cds_start": null,
"cds_end": null,
"cds_length": 2166,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000544951.6"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3416A>G",
"hgvs_p": "p.Asp1139Gly",
"transcript": "NM_001168272.2",
"protein_id": "NP_001161744.1",
"transcript_support_level": null,
"aa_start": 1139,
"aa_end": null,
"aa_length": 2743,
"cds_start": 3416,
"cds_end": null,
"cds_length": 8232,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001168272.2"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3434A>G",
"hgvs_p": "p.Asp1145Gly",
"transcript": "NM_001099952.4",
"protein_id": "NP_001093422.2",
"transcript_support_level": null,
"aa_start": 1145,
"aa_end": null,
"aa_length": 2710,
"cds_start": 3434,
"cds_end": null,
"cds_length": 8133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001099952.4"
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3389A>G",
"hgvs_p": "p.Asp1130Gly",
"transcript": "NM_002222.7",
"protein_id": "NP_002213.5",
"transcript_support_level": null,
"aa_start": 1130,
"aa_end": null,
"aa_length": 2695,
"cds_start": 3389,
"cds_end": null,
"cds_length": 8088,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002222.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "n.3434A>G",
"hgvs_p": null,
"transcript": "ENST00000302640.13",
"protein_id": "ENSP00000306253.9",
"transcript_support_level": 5,
"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": "nonsense_mediated_decay",
"feature": "ENST00000302640.13"
},
{
"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": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "n.173A>G",
"hgvs_p": null,
"transcript": "ENST00000647624.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000647624.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "n.962A>G",
"hgvs_p": null,
"transcript": "ENST00000647717.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000647717.1"
}
],
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"dbsnp": "rs61751570",
"frequency_reference_population": 0.0014306179,
"hom_count_reference_population": 4,
"allele_count_reference_population": 2309,
"gnomad_exomes_af": 0.00141483,
"gnomad_genomes_af": 0.00158213,
"gnomad_exomes_ac": 2068,
"gnomad_genomes_ac": 241,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.007781893014907837,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.422,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1016,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.11,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.432,
"phylop100way_prediction": "Uncertain_significance",
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001378452.1",
"gene_symbol": "ITPR1",
"hgnc_id": 6180,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.3461A>G",
"hgvs_p": "p.Asp1154Gly"
}
],
"clinvar_disease": "Autosomal dominant cerebellar ataxia,Gillespie syndrome,Inborn genetic diseases,Spinocerebellar ataxia type 15/16,Spinocerebellar ataxia type 29,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:6 B:1",
"phenotype_combined": "Autosomal dominant cerebellar ataxia|Spinocerebellar ataxia type 29|not provided|Gillespie syndrome;Spinocerebellar ataxia type 29;Spinocerebellar ataxia type 15/16|Inborn genetic diseases",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}