11-117390772-C-G

Variant names:

• chr11-117390772-C-G
• rs897837
• NM_014956.5:c.1935-5C>G

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_014956.5(CEP164):​c.1935-5C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 1,613,500 control chromosomes in the GnomAD database, including 22,936 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.13 (1525 hom., cov: 31)
  • Exomes 𝑓: 0.17 (21411 hom.)
• Consequence: CEP164 NM_014956.5 splice_region, intron
• Scores: Splicing: ADA: 0.0005488
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:7
• Conservation: PhyloP100: 0.655

Genes affected

CEP164 (HGNC:29182): (centrosomal protein 164) This gene encodes a centrosomal protein involved in microtubule organization, DNA damage response, and chromosome segregation. The encoded protein is required for assembly of primary cilia and localizes to mature centrioles. Defects in this gene are a cause of nephronophthisis-related ciliopathies. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 11-117390772-C-G is Benign according to our data. Variant chr11-117390772-C-G is described in ClinVar as [Benign]. Clinvar id is 260476.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117390772-C-G is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP164	NM_014956.5	c.1935-5C>G		splice_region_variant, intron_variant	Intron 15 of 32	ENST00000278935.8	NP_055771.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP164	ENST00000278935.8	c.1935-5C>G		splice_region_variant, intron_variant	Intron 15 of 32	1	NM_014956.5	ENSP00000278935.3

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19367 AN: 151866 Hom.: 1524 Cov.: 31

Gnomad AFR AF: 0.0332

Gnomad AMI AF: 0.0973

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.134

GnomAD2 exomes AF: 0.169 AC: 42588 AN: 251290 AF XY: 0.170

Gnomad AFR exome AF: 0.0294

Gnomad AMR exome AF: 0.263

Gnomad ASJ exome AF: 0.190

Gnomad EAS exome AF: 0.124

Gnomad FIN exome AF: 0.145

Gnomad NFE exome AF: 0.164

Gnomad OTH exome AF: 0.181

GnomAD4 exome AF: 0.167 AC: 243902 AN: 1461516 Hom.: 21411 Cov.: 33 AF XY: 0.168 AC XY: 122187 AN XY: 727086

Gnomad4 AFR exome AF: 0.0292 AC: 977 AN: 33468

Gnomad4 AMR exome AF: 0.255 AC: 11406 AN: 44712

Gnomad4 ASJ exome AF: 0.197 AC: 5142 AN: 26130

Gnomad4 EAS exome AF: 0.115 AC: 4546 AN: 39700

Gnomad4 SAS exome AF: 0.201 AC: 17304 AN: 86236

Gnomad4 FIN exome AF: 0.146 AC: 7776 AN: 53404

Gnomad4 NFE exome AF: 0.168 AC: 186240 AN: 1111748

Gnomad4 Remaining exome AF: 0.156 AC: 9442 AN: 60370

GnomAD4 genome AF: 0.127 AC: 19371 AN: 151984 Hom.: 1525 Cov.: 31 AF XY: 0.129 AC XY: 9555 AN XY: 74266

Gnomad4 AFR AF: 0.0331 AC: 0.0330987 AN: 0.0330987

Gnomad4 AMR AF: 0.196 AC: 0.195755 AN: 0.195755

Gnomad4 ASJ AF: 0.186 AC: 0.185879 AN: 0.185879

Gnomad4 EAS AF: 0.126 AC: 0.126021 AN: 0.126021

Gnomad4 SAS AF: 0.184 AC: 0.18386 AN: 0.18386

Gnomad4 FIN AF: 0.138 AC: 0.138199 AN: 0.138199

Gnomad4 NFE AF: 0.161 AC: 0.161394 AN: 0.161394

Gnomad4 OTH AF: 0.133 AC: 0.132923 AN: 0.132923

Alfa AF: 0.156 Hom.: 660

Bravo AF: 0.130

Asia WGS AF: 0.130 AC: 450 AN: 3478

EpiCase AF: 0.162

EpiControl AF: 0.157

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:3

-

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

-

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Nephronophthisis 15 Benign:2

Jul 22, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

May 04, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.7
DANN	Benign	0.34
Mutation Taster		=99/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00055
dbscSNV1_RF	Benign	0.070
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs897837; hg19: chr11-117261488; COSMIC: COSV54038326;