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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: 13-52144720-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=52144720&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 52144720,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001424264.1",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.775C>G",
"hgvs_p": "p.Arg259Gly",
"transcript": "NM_002498.3",
"protein_id": "NP_002489.1",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 506,
"cds_start": 775,
"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": "R",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.775C>G",
"hgvs_p": "p.Arg259Gly",
"transcript": "ENST00000610828.5",
"protein_id": "ENSP00000480328.1",
"transcript_support_level": 1,
"aa_start": 259,
"aa_end": null,
"aa_length": 506,
"cds_start": 775,
"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": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.793C>G",
"hgvs_p": "p.Arg265Gly",
"transcript": "NM_001424264.1",
"protein_id": "NP_001411193.1",
"transcript_support_level": null,
"aa_start": 265,
"aa_end": null,
"aa_length": 512,
"cds_start": 793,
"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": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.793C>G",
"hgvs_p": "p.Arg265Gly",
"transcript": "ENST00000962649.1",
"protein_id": "ENSP00000632708.1",
"transcript_support_level": null,
"aa_start": 265,
"aa_end": null,
"aa_length": 512,
"cds_start": 793,
"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": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.775C>G",
"hgvs_p": "p.Arg259Gly",
"transcript": "NM_001424265.1",
"protein_id": "NP_001411194.1",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 506,
"cds_start": 775,
"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": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.775C>G",
"hgvs_p": "p.Arg259Gly",
"transcript": "NM_001424266.1",
"protein_id": "NP_001411195.1",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 506,
"cds_start": 775,
"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": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.775C>G",
"hgvs_p": "p.Arg259Gly",
"transcript": "NM_152720.3",
"protein_id": "NP_689933.1",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 506,
"cds_start": 775,
"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": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.775C>G",
"hgvs_p": "p.Arg259Gly",
"transcript": "ENST00000618534.4",
"protein_id": "ENSP00000484443.1",
"transcript_support_level": 5,
"aa_start": 259,
"aa_end": null,
"aa_length": 506,
"cds_start": 775,
"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": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.775C>G",
"hgvs_p": "p.Arg259Gly",
"transcript": "ENST00000858785.1",
"protein_id": "ENSP00000528844.1",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 506,
"cds_start": 775,
"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": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.775C>G",
"hgvs_p": "p.Arg259Gly",
"transcript": "ENST00000858786.1",
"protein_id": "ENSP00000528845.1",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 506,
"cds_start": 775,
"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": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.775C>G",
"hgvs_p": "p.Arg259Gly",
"transcript": "ENST00000858787.1",
"protein_id": "ENSP00000528846.1",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 506,
"cds_start": 775,
"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": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.757C>G",
"hgvs_p": "p.Arg253Gly",
"transcript": "ENST00000913399.1",
"protein_id": "ENSP00000583458.1",
"transcript_support_level": null,
"aa_start": 253,
"aa_end": null,
"aa_length": 500,
"cds_start": 757,
"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": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.775C>G",
"hgvs_p": "p.Arg259Gly",
"transcript": "ENST00000620675.4",
"protein_id": "ENSP00000481533.1",
"transcript_support_level": 5,
"aa_start": 259,
"aa_end": null,
"aa_length": 497,
"cds_start": 775,
"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": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.775C>G",
"hgvs_p": "p.Arg259Gly",
"transcript": "NM_001424268.1",
"protein_id": "NP_001411197.1",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 489,
"cds_start": 775,
"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": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.775C>G",
"hgvs_p": "p.Arg259Gly",
"transcript": "NM_001424269.1",
"protein_id": "NP_001411198.1",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 489,
"cds_start": 775,
"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": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.775C>G",
"hgvs_p": "p.Arg259Gly",
"transcript": "ENST00000913401.1",
"protein_id": "ENSP00000583460.1",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 488,
"cds_start": 775,
"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": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.640C>G",
"hgvs_p": "p.Arg214Gly",
"transcript": "ENST00000913403.1",
"protein_id": "ENSP00000583462.1",
"transcript_support_level": null,
"aa_start": 214,
"aa_end": null,
"aa_length": 461,
"cds_start": 640,
"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": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.775C>G",
"hgvs_p": "p.Arg259Gly",
"transcript": "ENST00000962648.1",
"protein_id": "ENSP00000632707.1",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 458,
"cds_start": 775,
"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": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.607C>G",
"hgvs_p": "p.Arg203Gly",
"transcript": "NM_001424254.1",
"protein_id": "NP_001411183.1",
"transcript_support_level": null,
"aa_start": 203,
"aa_end": null,
"aa_length": 450,
"cds_start": 607,
"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": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.607C>G",
"hgvs_p": "p.Arg203Gly",
"transcript": "NM_001424270.1",
"protein_id": "NP_001411199.1",
"transcript_support_level": null,
"aa_start": 203,
"aa_end": null,
"aa_length": 433,
"cds_start": 607,
"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": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.541C>G",
"hgvs_p": "p.Arg181Gly",
"transcript": "NM_001424255.1",
"protein_id": "NP_001411184.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 428,
"cds_start": 541,
"cds_end": null,
"cds_length": 1287,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001424255.1"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK3",
"gene_hgnc_id": 7746,
"hgvs_c": "c.541C>G",
"hgvs_p": "p.Arg181Gly",
"transcript": "NM_001424257.1",
"protein_id": "NP_001411186.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 428,
"cds_start": 541,
"cds_end": null,
"cds_length": 1287,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001424257.1"
},
{
"aa_ref": "R",
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{
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},
{
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"protein_coding": true,
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"missense_variant"
],
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"gene_symbol": "NEK3",
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"hgvs_c": "c.445C>G",
"hgvs_p": "p.Arg149Gly",
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"biotype": "protein_coding",
"feature": "NM_001424259.1"
},
{
"aa_ref": null,
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"intron_variant"
],
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"feature": "ENST00000913402.1"
},
{
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"non_coding_transcript_exon_variant"
],
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{
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"non_coding_transcript_exon_variant"
],
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},
{
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"consequences": [
"downstream_gene_variant"
],
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"gene_symbol": "NEK3",
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"hgvs_c": "n.*540C>G",
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"transcript": "ENST00000551355.5",
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"biotype": "nonsense_mediated_decay",
"feature": "ENST00000551355.5"
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],
"gene_symbol": "NEK3",
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"dbsnp": "rs34077016",
"frequency_reference_population": 0.0009685263,
"hom_count_reference_population": 15,
"allele_count_reference_population": 1563,
"gnomad_exomes_af": 0.000650636,
"gnomad_genomes_af": 0.00402245,
"gnomad_exomes_ac": 951,
"gnomad_genomes_ac": 612,
"gnomad_exomes_homalt": 12,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.00939255952835083,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.038,
"revel_prediction": "Benign",
"alphamissense_score": 0.0846,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.412,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001424264.1",
"gene_symbol": "NEK3",
"hgnc_id": 7746,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.793C>G",
"hgvs_p": "p.Arg265Gly"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}