rs3017608

Positions:

• chr11-117318500-G-A

Variant summary

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

The ENST00000504906.1(ENSG00000250699):​n.342-1992C>T variant causes a intron, non coding transcript 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: ENST00000504906.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.589

Genes affected

(HGNC:):

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=-0.98).
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000504906.1	n.342-1992C>T		intron_variant, non_coding_transcript_variant		3
CEP164	ENST00000525734.5	c.-98+3772G>A		intron_variant		2		ENSP00000436609

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

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.799

Gnomad4 SAS AF: 0.635

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.500

Alfa AF: 0.468 Hom.: 1559

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3017608; hg19: chr11-117189216;