rs3017608

Variant names:

• chr11-117318500-G-A
• rs3017608
• ENST00000525734.5:c.-98+3772G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-117318500-G-A
• chr11-117318500-G-T

Variant summary

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

The ENST00000525734.5(CEP164):​c.-98+3772G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 150,336 control chromosomes in the GnomAD database, including 18,466 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 0.49 (18466 hom., cov: 28)
• Consequence: CEP164 ENST00000525734.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.589
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 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+3772G>A		intron_variant	Intron 1 of 4	2		ENSP00000436609.1
ENSG00000250699	ENST00000504906.1	n.342-1992C>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.491 AC: 73700 AN: 150220 Hom.: 18460 Cov.: 28

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.491 AC: 73743 AN: 150336 Hom.: 18466 Cov.: 28 AF XY: 0.494 AC XY: 36227 AN XY: 73322

African (AFR) AF: 0.472 AC: 19254 AN: 40768

American (AMR) AF: 0.571 AC: 8637 AN: 15118

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1727 AN: 3460

East Asian (EAS) AF: 0.799 AC: 4095 AN: 5122

South Asian (SAS) AF: 0.635 AC: 3037 AN: 4782

European-Finnish (FIN) AF: 0.441 AC: 4462 AN: 10128

Middle Eastern (MID) AF: 0.503 AC: 146 AN: 290

European-Non Finnish (NFE) AF: 0.455 AC: 30814 AN: 67678

Other (OTH) AF: 0.500 AC: 1042 AN: 2082

Alfa AF: 0.456 Hom.: 1981

Bravo AF: 0.496

Asia WGS AF: 0.690 AC: 2398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.4
DANN	Benign	0.38
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs3017608; hg19: chr11-117189216;