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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: 20-3223409-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=3223409&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 3223409,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000380113.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"hgvs_c": "c.532C>T",
"hgvs_p": "p.Arg178Cys",
"transcript": "NM_033453.4",
"protein_id": "NP_258412.1",
"transcript_support_level": null,
"aa_start": 178,
"aa_end": null,
"aa_length": 194,
"cds_start": 532,
"cds_end": null,
"cds_length": 585,
"cdna_start": 586,
"cdna_end": null,
"cdna_length": 1037,
"mane_select": "ENST00000380113.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"hgvs_c": "c.532C>T",
"hgvs_p": "p.Arg178Cys",
"transcript": "ENST00000380113.8",
"protein_id": "ENSP00000369456.3",
"transcript_support_level": 1,
"aa_start": 178,
"aa_end": null,
"aa_length": 194,
"cds_start": 532,
"cds_end": null,
"cds_length": 585,
"cdna_start": 586,
"cdna_end": null,
"cdna_length": 1037,
"mane_select": "NM_033453.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"hgvs_c": "c.481C>T",
"hgvs_p": "p.Arg161Cys",
"transcript": "ENST00000455664.6",
"protein_id": "ENSP00000413282.1",
"transcript_support_level": 1,
"aa_start": 161,
"aa_end": null,
"aa_length": 177,
"cds_start": 481,
"cds_end": null,
"cds_length": 534,
"cdna_start": 520,
"cdna_end": null,
"cdna_length": 729,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"hgvs_c": "c.409C>T",
"hgvs_p": "p.Arg137Cys",
"transcript": "ENST00000399838.3",
"protein_id": "ENSP00000382732.3",
"transcript_support_level": 1,
"aa_start": 137,
"aa_end": null,
"aa_length": 153,
"cds_start": 409,
"cds_end": null,
"cds_length": 462,
"cdna_start": 436,
"cdna_end": null,
"cdna_length": 897,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"hgvs_c": "c.658C>T",
"hgvs_p": "p.Arg220Cys",
"transcript": "NM_001424409.1",
"protein_id": "NP_001411338.1",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 236,
"cds_start": 658,
"cds_end": null,
"cds_length": 711,
"cdna_start": 998,
"cdna_end": null,
"cdna_length": 1449,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"hgvs_c": "c.481C>T",
"hgvs_p": "p.Arg161Cys",
"transcript": "NM_181493.4",
"protein_id": "NP_852470.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 177,
"cds_start": 481,
"cds_end": null,
"cds_length": 534,
"cdna_start": 535,
"cdna_end": null,
"cdna_length": 986,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"hgvs_c": "c.409C>T",
"hgvs_p": "p.Arg137Cys",
"transcript": "NM_001267623.2",
"protein_id": "NP_001254552.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 153,
"cds_start": 409,
"cds_end": null,
"cds_length": 462,
"cdna_start": 463,
"cdna_end": null,
"cdna_length": 914,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"hgvs_c": "c.579C>T",
"hgvs_p": "p.Ile193Ile",
"transcript": "NM_001424408.1",
"protein_id": "NP_001411337.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 238,
"cds_start": 579,
"cds_end": null,
"cds_length": 717,
"cdna_start": 633,
"cdna_end": null,
"cdna_length": 1084,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"hgvs_c": "c.195C>T",
"hgvs_p": "p.Ile65Ile",
"transcript": "NM_001324236.2",
"protein_id": "NP_001311165.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 110,
"cds_start": 195,
"cds_end": null,
"cds_length": 333,
"cdna_start": 589,
"cdna_end": null,
"cdna_length": 1040,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"hgvs_c": "c.195C>T",
"hgvs_p": "p.Ile65Ile",
"transcript": "NM_001324237.2",
"protein_id": "NP_001311166.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 110,
"cds_start": 195,
"cds_end": null,
"cds_length": 333,
"cdna_start": 824,
"cdna_end": null,
"cdna_length": 1275,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"hgvs_c": "c.195C>T",
"hgvs_p": "p.Ile65Ile",
"transcript": "NM_001324238.2",
"protein_id": "NP_001311167.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 110,
"cds_start": 195,
"cds_end": null,
"cds_length": 333,
"cdna_start": 827,
"cdna_end": null,
"cdna_length": 1278,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"hgvs_c": "c.195C>T",
"hgvs_p": "p.Ile65Ile",
"transcript": "NM_001351739.2",
"protein_id": "NP_001338668.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 110,
"cds_start": 195,
"cds_end": null,
"cds_length": 333,
"cdna_start": 507,
"cdna_end": null,
"cdna_length": 958,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"hgvs_c": "c.705C>T",
"hgvs_p": "p.Ile235Ile",
"transcript": "XM_047440139.1",
"protein_id": "XP_047296095.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 280,
"cds_start": 705,
"cds_end": null,
"cds_length": 843,
"cdna_start": 1045,
"cdna_end": null,
"cdna_length": 1496,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"hgvs_c": "c.456C>T",
"hgvs_p": "p.Ile152Ile",
"transcript": "XM_006723565.4",
"protein_id": "XP_006723628.1",
"transcript_support_level": null,
"aa_start": 152,
"aa_end": null,
"aa_length": 197,
"cds_start": 456,
"cds_end": null,
"cds_length": 594,
"cdna_start": 510,
"cdna_end": null,
"cdna_length": 961,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"hgvs_c": "n.506C>T",
"hgvs_p": null,
"transcript": "ENST00000460550.5",
"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": 967,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"hgvs_c": "n.338C>T",
"hgvs_p": null,
"transcript": "ENST00000461029.1",
"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": 378,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"hgvs_c": "n.209C>T",
"hgvs_p": null,
"transcript": "ENST00000472295.1",
"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": 670,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"hgvs_c": "n.567C>T",
"hgvs_p": null,
"transcript": "ENST00000483354.5",
"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": 1028,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"hgvs_c": "n.516C>T",
"hgvs_p": null,
"transcript": "ENST00000490838.6",
"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": 977,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"hgvs_c": "n.759C>T",
"hgvs_p": null,
"transcript": "NR_052000.2",
"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": 1210,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"hgvs_c": "n.521C>T",
"hgvs_p": null,
"transcript": "NR_052002.2",
"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": 972,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"hgvs_c": "c.412-3274C>T",
"hgvs_p": null,
"transcript": "NM_001324240.2",
"protein_id": "NP_001311169.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 138,
"cds_start": -4,
"cds_end": null,
"cds_length": 417,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1232,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ITPA",
"gene_hgnc_id": 6176,
"dbsnp": "rs746930990",
"frequency_reference_population": 0.0000012392925,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 6.8418e-7,
"gnomad_genomes_af": 0.00000656944,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9916197061538696,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.716,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8775,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.42,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.731,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000380113.8",
"gene_symbol": "ITPA",
"hgnc_id": 6176,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.532C>T",
"hgvs_p": "p.Arg178Cys"
}
],
"clinvar_disease": " 35,Developmental and epileptic encephalopathy,ITPA-related disorder,Inosine triphosphatase deficiency,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:2 US:1",
"phenotype_combined": "Developmental and epileptic encephalopathy, 35|Inosine triphosphatase deficiency|ITPA-related disorder|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}