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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-123613430-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=123613430&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 123613430,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001081550.2",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.4646A>G",
"hgvs_p": "p.Lys1549Arg",
"transcript": "NM_001081550.2",
"protein_id": "NP_001075019.1",
"transcript_support_level": null,
"aa_start": 1549,
"aa_end": null,
"aa_length": 1593,
"cds_start": 4646,
"cds_end": null,
"cds_length": 4782,
"cdna_start": 4676,
"cdna_end": null,
"cdna_length": 5600,
"mane_select": "ENST00000245838.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.4646A>G",
"hgvs_p": "p.Lys1549Arg",
"transcript": "ENST00000245838.13",
"protein_id": "ENSP00000245838.8",
"transcript_support_level": 5,
"aa_start": 1549,
"aa_end": null,
"aa_length": 1593,
"cds_start": 4646,
"cds_end": null,
"cds_length": 4782,
"cdna_start": 4676,
"cdna_end": null,
"cdna_length": 5600,
"mane_select": "NM_001081550.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.4646A>G",
"hgvs_p": "p.Lys1549Arg",
"transcript": "ENST00000355725.8",
"protein_id": "ENSP00000347959.4",
"transcript_support_level": 5,
"aa_start": 1549,
"aa_end": null,
"aa_length": 1593,
"cds_start": 4646,
"cds_end": null,
"cds_length": 4782,
"cdna_start": 4680,
"cdna_end": null,
"cdna_length": 4930,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.4301A>G",
"hgvs_p": "p.Lys1434Arg",
"transcript": "ENST00000491737.5",
"protein_id": "ENSP00000419795.1",
"transcript_support_level": 5,
"aa_start": 1434,
"aa_end": null,
"aa_length": 1478,
"cds_start": 4301,
"cds_end": null,
"cds_length": 4437,
"cdna_start": 4301,
"cdna_end": null,
"cdna_length": 4452,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.1109A>G",
"hgvs_p": "p.Lys370Arg",
"transcript": "ENST00000618150.4",
"protein_id": "ENSP00000480478.1",
"transcript_support_level": 1,
"aa_start": 370,
"aa_end": null,
"aa_length": 414,
"cds_start": 1109,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 1188,
"cdna_end": null,
"cdna_length": 3211,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.1028A>G",
"hgvs_p": "p.Lys343Arg",
"transcript": "ENST00000441692.5",
"protein_id": "ENSP00000415211.1",
"transcript_support_level": 5,
"aa_start": 343,
"aa_end": null,
"aa_length": 387,
"cds_start": 1028,
"cds_end": null,
"cds_length": 1164,
"cdna_start": 1030,
"cdna_end": null,
"cdna_length": 4364,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.431A>G",
"hgvs_p": "p.Lys144Arg",
"transcript": "ENST00000448128.5",
"protein_id": "ENSP00000397317.1",
"transcript_support_level": 5,
"aa_start": 144,
"aa_end": null,
"aa_length": 188,
"cds_start": 431,
"cds_end": null,
"cds_length": 567,
"cdna_start": 433,
"cdna_end": null,
"cdna_length": 1365,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.413A>G",
"hgvs_p": "p.Lys138Arg",
"transcript": "ENST00000416618.5",
"protein_id": "ENSP00000415244.1",
"transcript_support_level": 5,
"aa_start": 138,
"aa_end": null,
"aa_length": 180,
"cds_start": 413,
"cds_end": null,
"cds_length": 543,
"cdna_start": 413,
"cdna_end": null,
"cdna_length": 657,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.125A>G",
"hgvs_p": "p.Lys42Arg",
"transcript": "ENST00000455053.5",
"protein_id": "ENSP00000402168.1",
"transcript_support_level": 3,
"aa_start": 42,
"aa_end": null,
"aa_length": 84,
"cds_start": 125,
"cds_end": null,
"cds_length": 255,
"cdna_start": 125,
"cdna_end": null,
"cdna_length": 573,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "n.*888A>G",
"hgvs_p": null,
"transcript": "ENST00000432353.5",
"protein_id": "ENSP00000415947.1",
"transcript_support_level": 1,
"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": 3188,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "n.*888A>G",
"hgvs_p": null,
"transcript": "ENST00000432353.5",
"protein_id": "ENSP00000415947.1",
"transcript_support_level": 1,
"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": 3188,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.4727A>G",
"hgvs_p": "p.Lys1576Arg",
"transcript": "NM_001441235.1",
"protein_id": "NP_001428164.1",
"transcript_support_level": null,
"aa_start": 1576,
"aa_end": null,
"aa_length": 1620,
"cds_start": 4727,
"cds_end": null,
"cds_length": 4863,
"cdna_start": 4757,
"cdna_end": null,
"cdna_length": 5681,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.4646A>G",
"hgvs_p": "p.Lys1549Arg",
"transcript": "NM_001441236.1",
"protein_id": "NP_001428165.1",
"transcript_support_level": null,
"aa_start": 1549,
"aa_end": null,
"aa_length": 1593,
"cds_start": 4646,
"cds_end": null,
"cds_length": 4782,
"cdna_start": 4676,
"cdna_end": null,
"cdna_length": 8010,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.4805A>G",
"hgvs_p": "p.Lys1602Arg",
"transcript": "XM_047442263.1",
"protein_id": "XP_047298219.1",
"transcript_support_level": null,
"aa_start": 1602,
"aa_end": null,
"aa_length": 1646,
"cds_start": 4805,
"cds_end": null,
"cds_length": 4941,
"cdna_start": 4835,
"cdna_end": null,
"cdna_length": 5759,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.4805A>G",
"hgvs_p": "p.Lys1602Arg",
"transcript": "XM_047442264.1",
"protein_id": "XP_047298220.1",
"transcript_support_level": null,
"aa_start": 1602,
"aa_end": null,
"aa_length": 1646,
"cds_start": 4805,
"cds_end": null,
"cds_length": 4941,
"cdna_start": 4835,
"cdna_end": null,
"cdna_length": 8169,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.4805A>G",
"hgvs_p": "p.Lys1602Arg",
"transcript": "XM_047442265.1",
"protein_id": "XP_047298221.1",
"transcript_support_level": null,
"aa_start": 1602,
"aa_end": null,
"aa_length": 1644,
"cds_start": 4805,
"cds_end": null,
"cds_length": 4935,
"cdna_start": 4835,
"cdna_end": null,
"cdna_length": 5753,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.4805A>G",
"hgvs_p": "p.Lys1602Arg",
"transcript": "XM_047442266.1",
"protein_id": "XP_047298222.1",
"transcript_support_level": null,
"aa_start": 1602,
"aa_end": null,
"aa_length": 1644,
"cds_start": 4805,
"cds_end": null,
"cds_length": 4935,
"cdna_start": 4835,
"cdna_end": null,
"cdna_length": 8163,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.4793A>G",
"hgvs_p": "p.Lys1598Arg",
"transcript": "XM_047442267.1",
"protein_id": "XP_047298223.1",
"transcript_support_level": null,
"aa_start": 1598,
"aa_end": null,
"aa_length": 1642,
"cds_start": 4793,
"cds_end": null,
"cds_length": 4929,
"cdna_start": 4823,
"cdna_end": null,
"cdna_length": 5747,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.4739A>G",
"hgvs_p": "p.Lys1580Arg",
"transcript": "XM_047442268.1",
"protein_id": "XP_047298224.1",
"transcript_support_level": null,
"aa_start": 1580,
"aa_end": null,
"aa_length": 1624,
"cds_start": 4739,
"cds_end": null,
"cds_length": 4875,
"cdna_start": 4769,
"cdna_end": null,
"cdna_length": 5693,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.4739A>G",
"hgvs_p": "p.Lys1580Arg",
"transcript": "XM_047442269.1",
"protein_id": "XP_047298225.1",
"transcript_support_level": null,
"aa_start": 1580,
"aa_end": null,
"aa_length": 1624,
"cds_start": 4739,
"cds_end": null,
"cds_length": 4875,
"cdna_start": 4769,
"cdna_end": null,
"cdna_length": 8103,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.4724A>G",
"hgvs_p": "p.Lys1575Arg",
"transcript": "XM_047442271.1",
"protein_id": "XP_047298227.1",
"transcript_support_level": null,
"aa_start": 1575,
"aa_end": null,
"aa_length": 1619,
"cds_start": 4724,
"cds_end": null,
"cds_length": 4860,
"cdna_start": 4754,
"cdna_end": null,
"cdna_length": 5678,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
"hgvs_c": "c.4724A>G",
"hgvs_p": "p.Lys1575Arg",
"transcript": "XM_047442272.1",
"protein_id": "XP_047298228.1",
"transcript_support_level": null,
"aa_start": 1575,
"aa_end": null,
"aa_length": 1619,
"cds_start": 4724,
"cds_end": null,
"cds_length": 4860,
"cdna_start": 4754,
"cdna_end": null,
"cdna_length": 8088,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THOC2",
"gene_hgnc_id": 19073,
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],
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}
],
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"dbsnp": "rs1603229932",
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"computational_score_selected": 0.2047124207019806,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
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"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
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"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
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"phylop100way_prediction": "Benign",
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"spliceai_max_prediction": "Benign",
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"acmg_score": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 1,
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"pathogenic_score": 3,
"criteria": [
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"PP2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001081550.2",
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"effects": [
"missense_variant"
],
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],
"clinvar_disease": "X-linked intellectual disability-short stature-overweight syndrome",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "X-linked intellectual disability-short stature-overweight syndrome",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}