rs11186856

chr10-92204260-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_014912.5(CPEB3):c.1006-11624T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 148,354 control chromosomes in the GnomAD database, including 5,052 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 0.24 (5049 hom., cov: 32)
  • Exomes 𝑓: 0.57 (3 hom.)
• Consequence: CPEB3 NM_014912.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.90

Genes affected

CPEB3 (HGNC:21746): (cytoplasmic polyadenylation element binding protein 3) Enables mRNA 3'-UTR binding activity and translation factor activity, RNA binding. Involved in cellular response to amino acid stimulus; negative regulation of transcription by RNA polymerase II; and positive regulation of mRNA catabolic process. Located in several cellular components, including cytosol; midbody; and nucleoplasm. Part of CCR4-NOT complex. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPEB3	NM_014912.5	c.1006-11624T>C		intron_variant		ENST00000265997.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPEB3	ENST00000265997.5	c.1006-11624T>C		intron_variant		1	NM_014912.5
CPEB3	ENST00000412050.8	c.1006-11624T>C		intron_variant		1		P1
	ENST00000408115.1	n.47T>C		non_coding_transcript_exon_variant	1/1
CPEB3	ENST00000614585.4	c.1006-11624T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.245 AC: 36295 AN: 148222 Hom.: 5054 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.289

GnomAD4 exome AF: 0.571 AC: 8 AN: 14 Hom.: 3 Cov.: 0 AF XY: 0.571 AC XY: 8 AN XY: 14

Gnomad4 NFE exome AF: 0.700

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.245 AC: 36288 AN: 148340 Hom.: 5049 Cov.: 32 AF XY: 0.238 AC XY: 17307 AN XY: 72590

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.289

Alfa AF: 0.287 Hom.: 2781

Bravo AF: 0.239

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
Cadd	Benign	16
Dann	Benign	0.84

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: rs11186856; hg19: chr10-93964017;