rs1571176

Positions:

• chr10-92132396-C-A

Variant summary

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

The NM_014912.5(CPEB3):​c.1453+10633G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,878 control chromosomes in the GnomAD database, including 6,450 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 0.28 (6450 hom., cov: 32)
• Consequence: CPEB3 NM_014912.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CPEB3	NM_014912.5	c.1453+10633G>T		intron_variant		ENST00000265997.5	NP_055727.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CPEB3	ENST00000265997.5	c.1453+10633G>T		intron_variant		1	NM_014912.5	ENSP00000265997.4
CPEB3	ENST00000412050.8	c.1411+10633G>T		intron_variant		1		ENSP00000398310.2
CPEB3	ENST00000614585.4	c.1453+10633G>T		intron_variant		5		ENSP00000482128.1

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41787 AN: 151758 Hom.: 6456 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.275 AC: 41785 AN: 151878 Hom.: 6450 Cov.: 32 AF XY: 0.270 AC XY: 20076 AN XY: 74240

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.329

Alfa AF: 0.288 Hom.: 3432

Bravo AF: 0.285

Asia WGS AF: 0.192 AC: 669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.8
DANN	Benign	0.68

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: rs1571176; hg19: chr10-93892153; COSMIC: COSV56464143; COSMIC: COSV56464143;