ENST00000525734.5:c.-98+2107G>C

Variant names:

• chr11-117316835-G-C
• rs11601511
• ENST00000525734.5:c.-98+2107G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000525734.5(CEP164):​c.-98+2107G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,170 control chromosomes in the GnomAD database, including 1,963 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (1963 hom., cov: 32)
• Consequence: CEP164 ENST00000525734.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.538
• Publications: 4 publications found

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]

CEP164 Gene-Disease associations (from GenCC):

• ciliopathy

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• nephronophthisis 15

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine, Ambry Genetics, G2P
• Senior-Loken syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000250699 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP164	ENST00000525734.5	c.-98+2107G>C		intron_variant	Intron 1 of 4	2		ENSP00000436609.1
ENSG00000250699	ENST00000504906.1	n.342-327C>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23614 AN: 152052 Hom.: 1956 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0986

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.147

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.155 AC: 23637 AN: 152170 Hom.: 1963 Cov.: 32 AF XY: 0.155 AC XY: 11505 AN XY: 74362

African (AFR) AF: 0.161 AC: 6689 AN: 41524

American (AMR) AF: 0.0983 AC: 1502 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3472

East Asian (EAS) AF: 0.00289 AC: 15 AN: 5182

South Asian (SAS) AF: 0.139 AC: 671 AN: 4814

European-Finnish (FIN) AF: 0.200 AC: 2116 AN: 10584

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11588 AN: 67996

Other (OTH) AF: 0.149 AC: 314 AN: 2112

Alfa AF: 0.166 Hom.: 282

Bravo AF: 0.147

Asia WGS AF: 0.0750 AC: 263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.3
DANN	Benign	0.44
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs11601511; hg19: chr11-117187551;