rs11186872

chr10-92248823-G-A

Variant summary

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

The NM_014912.5(CPEB3):c.-11-8462C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 152,042 control chromosomes in the GnomAD database, including 7,975 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 0.32 (7975 hom., cov: 32)
• Consequence: CPEB3 NM_014912.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPEB3	NM_014912.5	c.-11-8462C>T		intron_variant		ENST00000265997.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPEB3	ENST00000265997.5	c.-11-8462C>T		intron_variant		1	NM_014912.5

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48172 AN: 151924 Hom.: 7971 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.317 AC: 48208 AN: 152042 Hom.: 7975 Cov.: 32 AF XY: 0.317 AC XY: 23561 AN XY: 74338

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.339

Alfa AF: 0.291 Hom.: 12258

Bravo AF: 0.336

Asia WGS AF: 0.348 AC: 1213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	8.4
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11186872; hg19: chr10-94008580;