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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: 1-40984966-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=40984966&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 40984966,
"ref": "A",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "NM_001905.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.312A>G",
"hgvs_p": "p.Gly104Gly",
"transcript": "NM_001905.4",
"protein_id": "NP_001896.2",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 591,
"cds_start": 312,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000650070.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001905.4"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.312A>G",
"hgvs_p": "p.Gly104Gly",
"transcript": "ENST00000650070.2",
"protein_id": "ENSP00000497602.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 591,
"cds_start": 312,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001905.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000650070.2"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.312A>G",
"hgvs_p": "p.Gly104Gly",
"transcript": "ENST00000372616.1",
"protein_id": "ENSP00000361699.1",
"transcript_support_level": 2,
"aa_start": 104,
"aa_end": null,
"aa_length": 591,
"cds_start": 312,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000372616.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.312A>G",
"hgvs_p": "p.Gly104Gly",
"transcript": "ENST00000470271.6",
"protein_id": "ENSP00000497901.2",
"transcript_support_level": 3,
"aa_start": 104,
"aa_end": null,
"aa_length": 591,
"cds_start": 312,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000470271.6"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.312A>G",
"hgvs_p": "p.Gly104Gly",
"transcript": "ENST00000649124.2",
"protein_id": "ENSP00000497744.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 591,
"cds_start": 312,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000649124.2"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.312A>G",
"hgvs_p": "p.Gly104Gly",
"transcript": "ENST00000870153.1",
"protein_id": "ENSP00000540212.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 591,
"cds_start": 312,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870153.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.312A>G",
"hgvs_p": "p.Gly104Gly",
"transcript": "ENST00000870154.1",
"protein_id": "ENSP00000540213.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 591,
"cds_start": 312,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870154.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.312A>G",
"hgvs_p": "p.Gly104Gly",
"transcript": "ENST00000870155.1",
"protein_id": "ENSP00000540214.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 591,
"cds_start": 312,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870155.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.312A>G",
"hgvs_p": "p.Gly104Gly",
"transcript": "ENST00000923258.1",
"protein_id": "ENSP00000593317.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 591,
"cds_start": 312,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923258.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.312A>G",
"hgvs_p": "p.Gly104Gly",
"transcript": "ENST00000960813.1",
"protein_id": "ENSP00000630872.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 591,
"cds_start": 312,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960813.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.312A>G",
"hgvs_p": "p.Gly104Gly",
"transcript": "ENST00000923259.1",
"protein_id": "ENSP00000593318.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 586,
"cds_start": 312,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923259.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.312A>G",
"hgvs_p": "p.Gly104Gly",
"transcript": "ENST00000649864.1",
"protein_id": "ENSP00000496792.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 564,
"cds_start": 312,
"cds_end": null,
"cds_length": 1695,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000649864.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.312A>G",
"hgvs_p": "p.Gly104Gly",
"transcript": "ENST00000870152.1",
"protein_id": "ENSP00000540211.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 540,
"cds_start": 312,
"cds_end": null,
"cds_length": 1623,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870152.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.312A>G",
"hgvs_p": "p.Gly104Gly",
"transcript": "ENST00000463285.7",
"protein_id": "ENSP00000497762.1",
"transcript_support_level": 3,
"aa_start": 104,
"aa_end": null,
"aa_length": 461,
"cds_start": 312,
"cds_end": null,
"cds_length": 1386,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000463285.7"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.333A>G",
"hgvs_p": "p.Gly111Gly",
"transcript": "XM_024453552.2",
"protein_id": "XP_024309320.1",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 598,
"cds_start": 333,
"cds_end": null,
"cds_length": 1797,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024453552.2"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.333A>G",
"hgvs_p": "p.Gly111Gly",
"transcript": "XM_047447461.1",
"protein_id": "XP_047303417.1",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 598,
"cds_start": 333,
"cds_end": null,
"cds_length": 1797,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447461.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.312A>G",
"hgvs_p": "p.Gly104Gly",
"transcript": "XM_024453553.2",
"protein_id": "XP_024309321.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 591,
"cds_start": 312,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024453553.2"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.312A>G",
"hgvs_p": "p.Gly104Gly",
"transcript": "XM_024453554.1",
"protein_id": "XP_024309322.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 591,
"cds_start": 312,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024453554.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.333A>G",
"hgvs_p": "p.Gly111Gly",
"transcript": "XM_047447469.1",
"protein_id": "XP_047303425.1",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 458,
"cds_start": 333,
"cds_end": null,
"cds_length": 1377,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447469.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.312A>G",
"hgvs_p": "p.Gly104Gly",
"transcript": "XM_047447471.1",
"protein_id": "XP_047303427.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 451,
"cds_start": 312,
"cds_end": null,
"cds_length": 1356,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447471.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.333A>G",
"hgvs_p": "p.Gly111Gly",
"transcript": "XM_024453561.2",
"protein_id": "XP_024309329.1",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 342,
"cds_start": 333,
"cds_end": null,
"cds_length": 1029,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024453561.2"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS1",
"gene_hgnc_id": 2519,
"hgvs_c": "c.312A>G",
"hgvs_p": "p.Gly104Gly",
"transcript": "XM_047447472.1",
"protein_id": "XP_047303428.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 335,
"cds_start": 312,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447472.1"
},
{
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],
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"computational_score_selected": -0.4399999976158142,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
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"alphamissense_score": null,
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"bayesdelnoaf_score": -0.44,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.036,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.05,
"spliceai_max_prediction": "Benign",
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"acmg_score": -9,
"acmg_classification": "Benign",
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"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
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"BP6_Moderate",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001905.4",
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"effects": [
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],
"inheritance_mode": "AR",
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],
"clinvar_disease": "CTPS1-related disorder,Severe combined immunodeficiency due to CTPS1 deficiency",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Severe combined immunodeficiency due to CTPS1 deficiency|CTPS1-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}