rs11601511

chr11-117316835-G-C

Variant summary

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

The ENST00000504906.1(ENSG00000250699):n.342-327C>G 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 0.155 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: ENST00000504906.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.538

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=-0.84).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000504906.1	n.342-327C>G		intron_variant, non_coding_transcript_variant		3
CEP164	ENST00000525734.5	c.-98+2107G>C		intron_variant		2

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

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.0983

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.00289

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.149

Alfa AF: 0.163 Hom.: 197

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11601511; hg19: chr11-117187551;