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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: 13-52136803-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=52136803&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 52136803,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001424264.1",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.1027A>G",
"hgvs_p": "p.Lys343Glu",
"transcript": "NM_002498.3",
"protein_id": "NP_002489.1",
"transcript_support_level": null,
"aa_start": 343,
"aa_end": null,
"aa_length": 506,
"cds_start": 1027,
"cds_end": null,
"cds_length": 1521,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000610828.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002498.3"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.1027A>G",
"hgvs_p": "p.Lys343Glu",
"transcript": "ENST00000610828.5",
"protein_id": "ENSP00000480328.1",
"transcript_support_level": 1,
"aa_start": 343,
"aa_end": null,
"aa_length": 506,
"cds_start": 1027,
"cds_end": null,
"cds_length": 1521,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002498.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000610828.5"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.1045A>G",
"hgvs_p": "p.Lys349Glu",
"transcript": "NM_001424264.1",
"protein_id": "NP_001411193.1",
"transcript_support_level": null,
"aa_start": 349,
"aa_end": null,
"aa_length": 512,
"cds_start": 1045,
"cds_end": null,
"cds_length": 1539,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001424264.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.1045A>G",
"hgvs_p": "p.Lys349Glu",
"transcript": "ENST00000962649.1",
"protein_id": "ENSP00000632708.1",
"transcript_support_level": null,
"aa_start": 349,
"aa_end": null,
"aa_length": 512,
"cds_start": 1045,
"cds_end": null,
"cds_length": 1539,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962649.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.1027A>G",
"hgvs_p": "p.Lys343Glu",
"transcript": "NM_001424265.1",
"protein_id": "NP_001411194.1",
"transcript_support_level": null,
"aa_start": 343,
"aa_end": null,
"aa_length": 506,
"cds_start": 1027,
"cds_end": null,
"cds_length": 1521,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001424265.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.1027A>G",
"hgvs_p": "p.Lys343Glu",
"transcript": "NM_001424266.1",
"protein_id": "NP_001411195.1",
"transcript_support_level": null,
"aa_start": 343,
"aa_end": null,
"aa_length": 506,
"cds_start": 1027,
"cds_end": null,
"cds_length": 1521,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001424266.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.1027A>G",
"hgvs_p": "p.Lys343Glu",
"transcript": "NM_152720.3",
"protein_id": "NP_689933.1",
"transcript_support_level": null,
"aa_start": 343,
"aa_end": null,
"aa_length": 506,
"cds_start": 1027,
"cds_end": null,
"cds_length": 1521,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_152720.3"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.1027A>G",
"hgvs_p": "p.Lys343Glu",
"transcript": "ENST00000618534.4",
"protein_id": "ENSP00000484443.1",
"transcript_support_level": 5,
"aa_start": 343,
"aa_end": null,
"aa_length": 506,
"cds_start": 1027,
"cds_end": null,
"cds_length": 1521,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000618534.4"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.1027A>G",
"hgvs_p": "p.Lys343Glu",
"transcript": "ENST00000858785.1",
"protein_id": "ENSP00000528844.1",
"transcript_support_level": null,
"aa_start": 343,
"aa_end": null,
"aa_length": 506,
"cds_start": 1027,
"cds_end": null,
"cds_length": 1521,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858785.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.1027A>G",
"hgvs_p": "p.Lys343Glu",
"transcript": "ENST00000858786.1",
"protein_id": "ENSP00000528845.1",
"transcript_support_level": null,
"aa_start": 343,
"aa_end": null,
"aa_length": 506,
"cds_start": 1027,
"cds_end": null,
"cds_length": 1521,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858786.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.1027A>G",
"hgvs_p": "p.Lys343Glu",
"transcript": "ENST00000858787.1",
"protein_id": "ENSP00000528846.1",
"transcript_support_level": null,
"aa_start": 343,
"aa_end": null,
"aa_length": 506,
"cds_start": 1027,
"cds_end": null,
"cds_length": 1521,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858787.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.1009A>G",
"hgvs_p": "p.Lys337Glu",
"transcript": "ENST00000913399.1",
"protein_id": "ENSP00000583458.1",
"transcript_support_level": null,
"aa_start": 337,
"aa_end": null,
"aa_length": 500,
"cds_start": 1009,
"cds_end": null,
"cds_length": 1503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913399.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.1027A>G",
"hgvs_p": "p.Lys343Glu",
"transcript": "ENST00000620675.4",
"protein_id": "ENSP00000481533.1",
"transcript_support_level": 5,
"aa_start": 343,
"aa_end": null,
"aa_length": 497,
"cds_start": 1027,
"cds_end": null,
"cds_length": 1494,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000620675.4"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.976A>G",
"hgvs_p": "p.Lys326Glu",
"transcript": "NM_001424268.1",
"protein_id": "NP_001411197.1",
"transcript_support_level": null,
"aa_start": 326,
"aa_end": null,
"aa_length": 489,
"cds_start": 976,
"cds_end": null,
"cds_length": 1470,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001424268.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.976A>G",
"hgvs_p": "p.Lys326Glu",
"transcript": "NM_001424269.1",
"protein_id": "NP_001411198.1",
"transcript_support_level": null,
"aa_start": 326,
"aa_end": null,
"aa_length": 489,
"cds_start": 976,
"cds_end": null,
"cds_length": 1470,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001424269.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.973A>G",
"hgvs_p": "p.Lys325Glu",
"transcript": "ENST00000913401.1",
"protein_id": "ENSP00000583460.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 488,
"cds_start": 973,
"cds_end": null,
"cds_length": 1467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913401.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.892A>G",
"hgvs_p": "p.Lys298Glu",
"transcript": "ENST00000913403.1",
"protein_id": "ENSP00000583462.1",
"transcript_support_level": null,
"aa_start": 298,
"aa_end": null,
"aa_length": 461,
"cds_start": 892,
"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": "ENST00000913403.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.1027A>G",
"hgvs_p": "p.Lys343Glu",
"transcript": "ENST00000962648.1",
"protein_id": "ENSP00000632707.1",
"transcript_support_level": null,
"aa_start": 343,
"aa_end": null,
"aa_length": 458,
"cds_start": 1027,
"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": "ENST00000962648.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.859A>G",
"hgvs_p": "p.Lys287Glu",
"transcript": "NM_001424254.1",
"protein_id": "NP_001411183.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 450,
"cds_start": 859,
"cds_end": null,
"cds_length": 1353,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001424254.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.826A>G",
"hgvs_p": "p.Lys276Glu",
"transcript": "ENST00000913402.1",
"protein_id": "ENSP00000583461.1",
"transcript_support_level": null,
"aa_start": 276,
"aa_end": null,
"aa_length": 439,
"cds_start": 826,
"cds_end": null,
"cds_length": 1320,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913402.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.808A>G",
"hgvs_p": "p.Lys270Glu",
"transcript": "NM_001424270.1",
"protein_id": "NP_001411199.1",
"transcript_support_level": null,
"aa_start": 270,
"aa_end": null,
"aa_length": 433,
"cds_start": 808,
"cds_end": null,
"cds_length": 1302,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001424270.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.793A>G",
"hgvs_p": "p.Lys265Glu",
"transcript": "NM_001424255.1",
"protein_id": "NP_001411184.1",
"transcript_support_level": null,
"aa_start": 265,
"aa_end": null,
"aa_length": 428,
"cds_start": 793,
"cds_end": null,
"cds_length": 1287,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
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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": "NM_001424271.1",
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"biotype": "protein_coding",
"feature": "NM_001424271.1"
},
{
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"missense_variant"
],
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"gene_symbol": "NEK3",
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"transcript": "NM_001424259.1",
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"biotype": "protein_coding",
"feature": "NM_001424259.1"
},
{
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],
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"feature": "ENST00000618856.1"
},
{
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"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
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"transcript": "ENST00000617054.1",
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"biotype": "nonsense_mediated_decay",
"feature": "ENST00000617054.1"
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{
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"consequences": [
"non_coding_transcript_exon_variant"
],
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"gene_symbol": "NEK3",
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"transcript": "NR_164641.1",
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"biotype": "pseudogene",
"feature": "NR_164641.1"
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
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"gene_symbol": "NEK3",
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"hgvs_c": "n.*80A>G",
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"transcript": "ENST00000617054.1",
"protein_id": "ENSP00000484594.1",
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"biotype": "nonsense_mediated_decay",
"feature": "ENST00000617054.1"
}
],
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"dbsnp": null,
"frequency_reference_population": 7.173241e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 7.17324e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.05234214663505554,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.023,
"revel_prediction": "Benign",
"alphamissense_score": 0.0627,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.166,
"phylop100way_prediction": "Benign",
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001424264.1",
"gene_symbol": "NEK3",
"hgnc_id": 7746,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1045A>G",
"hgvs_p": "p.Lys349Glu"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}