rs8258

chr11-117412960-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014956.5(CEP164):c.*792T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 152,122 control chromosomes in the GnomAD database, including 27,935 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 0.60 (27929 hom., cov: 32)
  • Exomes 𝑓: 0.67 (6 hom.)
• Consequence: CEP164 NM_014956.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.96

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP164	NM_014956.5	c.*792T>C		3_prime_UTR_variant	33/33	ENST00000278935.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP164	ENST00000278935.8	c.*792T>C		3_prime_UTR_variant	33/33	1	NM_014956.5	P1
CEP164	ENST00000533706.5	n.4729T>C		non_coding_transcript_exon_variant	27/27	5

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91133 AN: 151974 Hom.: 27894 Cov.: 32

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.602

GnomAD4 exome AF: 0.667 AC: 20 AN: 30 Hom.: 6 Cov.: 0 AF XY: 0.700 AC XY: 14 AN XY: 20

Gnomad4 FIN exome AF: 0.667

Gnomad4 NFE exome AF: 0.667

GnomAD4 genome AF: 0.600 AC: 91216 AN: 152092 Hom.: 27929 Cov.: 32 AF XY: 0.594 AC XY: 44148 AN XY: 74334

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.604

Alfa AF: 0.611 Hom.: 66541

Bravo AF: 0.587

Asia WGS AF: 0.460 AC: 1598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.060
Dann	Benign	0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs8258; hg19: chr11-117283676;