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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: 19-40374524-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=40374524&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 40374524,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000409735.9",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "NM_012268.4",
"protein_id": "NP_036400.2",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 490,
"cds_start": 923,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 1275,
"cdna_end": null,
"cdna_length": 2137,
"mane_select": "ENST00000409735.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "ENST00000409735.9",
"protein_id": "ENSP00000386938.3",
"transcript_support_level": 1,
"aa_start": 308,
"aa_end": null,
"aa_length": 490,
"cds_start": 923,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 1275,
"cdna_end": null,
"cdna_length": 2137,
"mane_select": "NM_012268.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "ENST00000356508.9",
"protein_id": "ENSP00000348901.5",
"transcript_support_level": 1,
"aa_start": 308,
"aa_end": null,
"aa_length": 490,
"cds_start": 923,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 1046,
"cdna_end": null,
"cdna_length": 1906,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "NM_001031696.4",
"protein_id": "NP_001026866.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 490,
"cds_start": 923,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 1051,
"cdna_end": null,
"cdna_length": 1913,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "NM_001291311.2",
"protein_id": "NP_001278240.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 490,
"cds_start": 923,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 1255,
"cdna_end": null,
"cdna_length": 2117,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "ENST00000409281.5",
"protein_id": "ENSP00000387022.1",
"transcript_support_level": 2,
"aa_start": 308,
"aa_end": null,
"aa_length": 490,
"cds_start": 923,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 1255,
"cdna_end": null,
"cdna_length": 2115,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "ENST00000409419.5",
"protein_id": "ENSP00000386293.1",
"transcript_support_level": 5,
"aa_start": 308,
"aa_end": null,
"aa_length": 490,
"cds_start": 923,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 1114,
"cdna_end": null,
"cdna_length": 1966,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "ENST00000409587.5",
"protein_id": "ENSP00000387050.1",
"transcript_support_level": 5,
"aa_start": 308,
"aa_end": null,
"aa_length": 490,
"cds_start": 923,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 1320,
"cdna_end": null,
"cdna_length": 2180,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "ENST00000700616.1",
"protein_id": "ENSP00000515107.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 490,
"cds_start": 923,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 1171,
"cdna_end": null,
"cdna_length": 5121,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "ENST00000700619.1",
"protein_id": "ENSP00000515110.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 490,
"cds_start": 923,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 1099,
"cdna_end": null,
"cdna_length": 2051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "ENST00000700620.1",
"protein_id": "ENSP00000515111.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 490,
"cds_start": 923,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 1099,
"cdna_end": null,
"cdna_length": 1806,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "ENST00000700621.1",
"protein_id": "ENSP00000515112.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 490,
"cds_start": 923,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 1125,
"cdna_end": null,
"cdna_length": 5075,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "ENST00000700623.1",
"protein_id": "ENSP00000515113.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 490,
"cds_start": 923,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 1007,
"cdna_end": null,
"cdna_length": 4705,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "ENST00000700625.1",
"protein_id": "ENSP00000515115.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 490,
"cds_start": 923,
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"cdna_start": 1124,
"cdna_end": null,
"cdna_length": 5074,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "ENST00000700626.1",
"protein_id": "ENSP00000515116.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 490,
"cds_start": 923,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 1112,
"cdna_end": null,
"cdna_length": 5062,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "ENST00000700628.1",
"protein_id": "ENSP00000515117.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 490,
"cds_start": 923,
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"cdna_start": 1039,
"cdna_end": null,
"cdna_length": 4989,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "ENST00000700630.1",
"protein_id": "ENSP00000515118.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 490,
"cds_start": 923,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 1812,
"cdna_end": null,
"cdna_length": 5762,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "ENST00000700631.1",
"protein_id": "ENSP00000515119.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 490,
"cds_start": 923,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 1152,
"cdna_end": null,
"cdna_length": 1918,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "ENST00000700632.1",
"protein_id": "ENSP00000515120.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 490,
"cds_start": 923,
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"cdna_start": 1152,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "ENST00000700633.1",
"protein_id": "ENSP00000515121.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 490,
"cds_start": 923,
"cds_end": null,
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"cdna_start": 1152,
"cdna_end": null,
"cdna_length": 1961,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "ENST00000700634.1",
"protein_id": "ENSP00000515122.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 490,
"cds_start": 923,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 1152,
"cdna_end": null,
"cdna_length": 1774,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro",
"transcript": "ENST00000700637.1",
"protein_id": "ENSP00000515123.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 490,
"cds_start": 923,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 1055,
"cdna_end": null,
"cdna_length": 1920,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD3",
"gene_hgnc_id": 17158,
"hgvs_c": "c.857T>C",
"hgvs_p": "p.Leu286Pro",
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{
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{
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},
{
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{
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},
{
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],
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"transcript": "ENST00000700639.1",
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}
],
"gene_symbol": "PLD3",
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"dbsnp": "rs537053537",
"frequency_reference_population": 0.000006815129,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000615648,
"gnomad_genomes_af": 0.0000131422,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9787353277206421,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.566,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9273,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.2,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.682,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Strong,BS2",
"acmg_by_gene": [
{
"score": 0,
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"pathogenic_score": 4,
"criteria": [
"PP3_Strong",
"BS2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000409735.9",
"gene_symbol": "PLD3",
"hgnc_id": 17158,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Leu308Pro"
}
],
"clinvar_disease": "Spinocerebellar ataxia 46",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Spinocerebellar ataxia 46",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}