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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: X-123626027-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=123626027&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 123626027,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001081550.2",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.2942G>A",
"hgvs_p": "p.Cys981Tyr",
"transcript": "NM_001081550.2",
"protein_id": "NP_001075019.1",
"transcript_support_level": null,
"aa_start": 981,
"aa_end": null,
"aa_length": 1593,
"cds_start": 2942,
"cds_end": null,
"cds_length": 4782,
"cdna_start": 2972,
"cdna_end": null,
"cdna_length": 5600,
"mane_select": "ENST00000245838.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.2942G>A",
"hgvs_p": "p.Cys981Tyr",
"transcript": "ENST00000245838.13",
"protein_id": "ENSP00000245838.8",
"transcript_support_level": 5,
"aa_start": 981,
"aa_end": null,
"aa_length": 1593,
"cds_start": 2942,
"cds_end": null,
"cds_length": 4782,
"cdna_start": 2972,
"cdna_end": null,
"cdna_length": 5600,
"mane_select": "NM_001081550.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.2942G>A",
"hgvs_p": "p.Cys981Tyr",
"transcript": "ENST00000355725.8",
"protein_id": "ENSP00000347959.4",
"transcript_support_level": 5,
"aa_start": 981,
"aa_end": null,
"aa_length": 1593,
"cds_start": 2942,
"cds_end": null,
"cds_length": 4782,
"cdna_start": 2976,
"cdna_end": null,
"cdna_length": 4930,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.2597G>A",
"hgvs_p": "p.Cys866Tyr",
"transcript": "ENST00000491737.5",
"protein_id": "ENSP00000419795.1",
"transcript_support_level": 5,
"aa_start": 866,
"aa_end": null,
"aa_length": 1478,
"cds_start": 2597,
"cds_end": null,
"cds_length": 4437,
"cdna_start": 2597,
"cdna_end": null,
"cdna_length": 4452,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.2942G>A",
"hgvs_p": "p.Cys981Tyr",
"transcript": "NM_001441235.1",
"protein_id": "NP_001428164.1",
"transcript_support_level": null,
"aa_start": 981,
"aa_end": null,
"aa_length": 1620,
"cds_start": 2942,
"cds_end": null,
"cds_length": 4863,
"cdna_start": 2972,
"cdna_end": null,
"cdna_length": 5681,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.2942G>A",
"hgvs_p": "p.Cys981Tyr",
"transcript": "NM_001441236.1",
"protein_id": "NP_001428165.1",
"transcript_support_level": null,
"aa_start": 981,
"aa_end": null,
"aa_length": 1593,
"cds_start": 2942,
"cds_end": null,
"cds_length": 4782,
"cdna_start": 2972,
"cdna_end": null,
"cdna_length": 8010,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.158G>A",
"hgvs_p": "p.Cys53Tyr",
"transcript": "ENST00000438358.1",
"protein_id": "ENSP00000416639.1",
"transcript_support_level": 5,
"aa_start": 53,
"aa_end": null,
"aa_length": 377,
"cds_start": 158,
"cds_end": null,
"cds_length": 1136,
"cdna_start": 159,
"cdna_end": null,
"cdna_length": 1137,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.2954G>A",
"hgvs_p": "p.Cys985Tyr",
"transcript": "XM_047442263.1",
"protein_id": "XP_047298219.1",
"transcript_support_level": null,
"aa_start": 985,
"aa_end": null,
"aa_length": 1646,
"cds_start": 2954,
"cds_end": null,
"cds_length": 4941,
"cdna_start": 2984,
"cdna_end": null,
"cdna_length": 5759,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.2954G>A",
"hgvs_p": "p.Cys985Tyr",
"transcript": "XM_047442264.1",
"protein_id": "XP_047298220.1",
"transcript_support_level": null,
"aa_start": 985,
"aa_end": null,
"aa_length": 1646,
"cds_start": 2954,
"cds_end": null,
"cds_length": 4941,
"cdna_start": 2984,
"cdna_end": null,
"cdna_length": 8169,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.2954G>A",
"hgvs_p": "p.Cys985Tyr",
"transcript": "XM_047442265.1",
"protein_id": "XP_047298221.1",
"transcript_support_level": null,
"aa_start": 985,
"aa_end": null,
"aa_length": 1644,
"cds_start": 2954,
"cds_end": null,
"cds_length": 4935,
"cdna_start": 2984,
"cdna_end": null,
"cdna_length": 5753,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.2954G>A",
"hgvs_p": "p.Cys985Tyr",
"transcript": "XM_047442266.1",
"protein_id": "XP_047298222.1",
"transcript_support_level": null,
"aa_start": 985,
"aa_end": null,
"aa_length": 1644,
"cds_start": 2954,
"cds_end": null,
"cds_length": 4935,
"cdna_start": 2984,
"cdna_end": null,
"cdna_length": 8163,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.2942G>A",
"hgvs_p": "p.Cys981Tyr",
"transcript": "XM_047442267.1",
"protein_id": "XP_047298223.1",
"transcript_support_level": null,
"aa_start": 981,
"aa_end": null,
"aa_length": 1642,
"cds_start": 2942,
"cds_end": null,
"cds_length": 4929,
"cdna_start": 2972,
"cdna_end": null,
"cdna_length": 5747,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.2954G>A",
"hgvs_p": "p.Cys985Tyr",
"transcript": "XM_047442268.1",
"protein_id": "XP_047298224.1",
"transcript_support_level": null,
"aa_start": 985,
"aa_end": null,
"aa_length": 1624,
"cds_start": 2954,
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"cds_length": 4875,
"cdna_start": 2984,
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"cdna_length": 5693,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
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"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.2954G>A",
"hgvs_p": "p.Cys985Tyr",
"transcript": "XM_047442269.1",
"protein_id": "XP_047298225.1",
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"cdna_start": 2984,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.2954G>A",
"hgvs_p": "p.Cys985Tyr",
"transcript": "XM_047442271.1",
"protein_id": "XP_047298227.1",
"transcript_support_level": null,
"aa_start": 985,
"aa_end": null,
"aa_length": 1619,
"cds_start": 2954,
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"cdna_start": 2984,
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"cdna_length": 5678,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.2954G>A",
"hgvs_p": "p.Cys985Tyr",
"transcript": "XM_047442272.1",
"protein_id": "XP_047298228.1",
"transcript_support_level": null,
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"cdna_start": 2984,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.2942G>A",
"hgvs_p": "p.Cys981Tyr",
"transcript": "XM_047442273.1",
"protein_id": "XP_047298229.1",
"transcript_support_level": null,
"aa_start": 981,
"aa_end": null,
"aa_length": 1615,
"cds_start": 2942,
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"cdna_start": 2972,
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"cdna_length": 5666,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.2954G>A",
"hgvs_p": "p.Cys985Tyr",
"transcript": "XM_017029679.2",
"protein_id": "XP_016885168.1",
"transcript_support_level": null,
"aa_start": 985,
"aa_end": null,
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"cds_start": 2954,
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"mane_select": null,
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"feature": null
},
{
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"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.2954G>A",
"hgvs_p": "p.Cys985Tyr",
"transcript": "XM_047442274.1",
"protein_id": "XP_047298230.1",
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"feature": null
},
{
"aa_ref": "C",
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.2942G>A",
"hgvs_p": "p.Cys981Tyr",
"transcript": "XM_047442275.1",
"protein_id": "XP_047298231.1",
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"aa_start": 981,
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.2318G>A",
"hgvs_p": "p.Cys773Tyr",
"transcript": "XM_047442277.1",
"protein_id": "XP_047298233.1",
"transcript_support_level": null,
"aa_start": 773,
"aa_end": null,
"aa_length": 1434,
"cds_start": 2318,
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"cds_length": 4305,
"cdna_start": 10630,
"cdna_end": null,
"cdna_length": 13405,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.2306G>A",
"hgvs_p": "p.Cys769Tyr",
"transcript": "XM_047442278.1",
"protein_id": "XP_047298234.1",
"transcript_support_level": null,
"aa_start": 769,
"aa_end": null,
"aa_length": 1430,
"cds_start": 2306,
"cds_end": null,
"cds_length": 4293,
"cdna_start": 10618,
"cdna_end": null,
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"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": 25,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "n.2984G>A",
"hgvs_p": null,
"transcript": "XR_007068195.1",
"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": 5187,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"dbsnp": "rs1556017474",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9575461149215698,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07999999821186066,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.978,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9992,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.59,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.86,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.08,
"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,PP2,PP3_Strong",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_001081550.2",
"gene_symbol": "THOC2",
"hgnc_id": 19073,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.2942G>A",
"hgvs_p": "p.Cys981Tyr"
}
],
"clinvar_disease": "Inborn genetic diseases,X-linked intellectual disability-short stature-overweight syndrome",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases|X-linked intellectual disability-short stature-overweight syndrome",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}