rs4938369

chr11-117317404-C-T

Variant summary

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

The ENST00000504906.1(ENSG00000250699):n.342-896G>A 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 0.0747 in 152,074 control chromosomes in the GnomAD database, including 601 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 0.075 (601 hom., cov: 32)
• Consequence: ENST00000504906.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000504906.1	n.342-896G>A		intron_variant, non_coding_transcript_variant		3
CEP164	ENST00000525734.5	c.-98+2676C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0747 AC: 11347 AN: 151956 Hom.: 602 Cov.: 32

Gnomad AFR AF: 0.0176

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.0888

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0805

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0747 AC: 11354 AN: 152074 Hom.: 601 Cov.: 32 AF XY: 0.0789 AC XY: 5865 AN XY: 74326

Gnomad4 AFR AF: 0.0176

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.0524

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.0885

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.0805

Gnomad4 OTH AF: 0.0677

Alfa AF: 0.0717 Hom.: 50

Bravo AF: 0.0750

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.96
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4938369; hg19: chr11-117188120;