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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: 3-4691145-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=4691145&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 4691145,
"ref": "T",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_001378452.1",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3830T>A",
"hgvs_p": "p.Ile1277Asn",
"transcript": "NM_001378452.1",
"protein_id": "NP_001365381.1",
"transcript_support_level": null,
"aa_start": 1277,
"aa_end": null,
"aa_length": 2758,
"cds_start": 3830,
"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": "I",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3830T>A",
"hgvs_p": "p.Ile1277Asn",
"transcript": "ENST00000649015.2",
"protein_id": "ENSP00000497605.1",
"transcript_support_level": null,
"aa_start": 1277,
"aa_end": null,
"aa_length": 2758,
"cds_start": 3830,
"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": "I",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3803T>A",
"hgvs_p": "p.Ile1268Asn",
"transcript": "ENST00000354582.12",
"protein_id": "ENSP00000346595.8",
"transcript_support_level": 5,
"aa_start": 1268,
"aa_end": null,
"aa_length": 2750,
"cds_start": 3803,
"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": "I",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3803T>A",
"hgvs_p": "p.Ile1268Asn",
"transcript": "ENST00000648266.1",
"protein_id": "ENSP00000498014.1",
"transcript_support_level": null,
"aa_start": 1268,
"aa_end": null,
"aa_length": 2749,
"cds_start": 3803,
"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": "I",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3785T>A",
"hgvs_p": "p.Ile1262Asn",
"transcript": "ENST00000650294.1",
"protein_id": "ENSP00000498056.1",
"transcript_support_level": null,
"aa_start": 1262,
"aa_end": null,
"aa_length": 2744,
"cds_start": 3785,
"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": "I",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3785T>A",
"hgvs_p": "p.Ile1262Asn",
"transcript": "ENST00000443694.5",
"protein_id": "ENSP00000401671.2",
"transcript_support_level": 1,
"aa_start": 1262,
"aa_end": null,
"aa_length": 2743,
"cds_start": 3785,
"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": "I",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3758T>A",
"hgvs_p": "p.Ile1253Asn",
"transcript": "ENST00000648309.1",
"protein_id": "ENSP00000497026.1",
"transcript_support_level": null,
"aa_start": 1253,
"aa_end": null,
"aa_length": 2734,
"cds_start": 3758,
"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": "I",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3803T>A",
"hgvs_p": "p.Ile1268Asn",
"transcript": "ENST00000357086.10",
"protein_id": "ENSP00000349597.4",
"transcript_support_level": 1,
"aa_start": 1268,
"aa_end": null,
"aa_length": 2710,
"cds_start": 3803,
"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": "I",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3758T>A",
"hgvs_p": "p.Ile1253Asn",
"transcript": "ENST00000456211.8",
"protein_id": "ENSP00000397885.2",
"transcript_support_level": 1,
"aa_start": 1253,
"aa_end": null,
"aa_length": 2695,
"cds_start": 3758,
"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": "I",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.1640T>A",
"hgvs_p": "p.Ile547Asn",
"transcript": "ENST00000648038.1",
"protein_id": "ENSP00000497872.1",
"transcript_support_level": null,
"aa_start": 547,
"aa_end": null,
"aa_length": 2012,
"cds_start": 1640,
"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": "I",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.1130T>A",
"hgvs_p": "p.Ile377Asn",
"transcript": "ENST00000648431.1",
"protein_id": "ENSP00000498149.1",
"transcript_support_level": null,
"aa_start": 377,
"aa_end": null,
"aa_length": 1817,
"cds_start": 1130,
"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": "I",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.737T>A",
"hgvs_p": "p.Ile246Asn",
"transcript": "ENST00000648212.1",
"protein_id": "ENSP00000498022.1",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 1738,
"cds_start": 737,
"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+37259T>A",
"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": "I",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3785T>A",
"hgvs_p": "p.Ile1262Asn",
"transcript": "NM_001168272.2",
"protein_id": "NP_001161744.1",
"transcript_support_level": null,
"aa_start": 1262,
"aa_end": null,
"aa_length": 2743,
"cds_start": 3785,
"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": "I",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3803T>A",
"hgvs_p": "p.Ile1268Asn",
"transcript": "NM_001099952.4",
"protein_id": "NP_001093422.2",
"transcript_support_level": null,
"aa_start": 1268,
"aa_end": null,
"aa_length": 2710,
"cds_start": 3803,
"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": "I",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.3758T>A",
"hgvs_p": "p.Ile1253Asn",
"transcript": "NM_002222.7",
"protein_id": "NP_002213.5",
"transcript_support_level": null,
"aa_start": 1253,
"aa_end": null,
"aa_length": 2695,
"cds_start": 3758,
"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": "I",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "c.161T>A",
"hgvs_p": "p.Ile54Asn",
"transcript": "ENST00000648016.1",
"protein_id": "ENSP00000496893.1",
"transcript_support_level": null,
"aa_start": 54,
"aa_end": null,
"aa_length": 1547,
"cds_start": 161,
"cds_end": null,
"cds_length": 4644,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000648016.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "n.3803T>A",
"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": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "n.542T>A",
"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": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "n.1331T>A",
"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"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"hgvs_c": "n.-179T>A",
"hgvs_p": null,
"transcript": "ENST00000647673.1",
"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": "ENST00000647673.1"
}
],
"gene_symbol": "ITPR1",
"gene_hgnc_id": 6180,
"dbsnp": "rs773030719",
"frequency_reference_population": 0.000026168062,
"hom_count_reference_population": 0,
"allele_count_reference_population": 42,
"gnomad_exomes_af": 0.0000282216,
"gnomad_genomes_af": 0.00000656935,
"gnomad_exomes_ac": 41,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9170242547988892,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.36399999260902405,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.898,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.5926,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.26,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.947,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.04,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.375760932046666,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate,BS1_Supporting",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate",
"BS1_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001378452.1",
"gene_symbol": "ITPR1",
"hgnc_id": 6180,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.3830T>A",
"hgvs_p": "p.Ile1277Asn"
}
],
"clinvar_disease": "Gillespie syndrome,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:7",
"phenotype_combined": "not specified|Gillespie syndrome|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}