rs1571176

Variant names:

• chr10-92132396-C-A
• rs1571176
• NM_014912.5:c.1453+10633G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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]

CPEB3 Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CPEB3	NM_014912.5	c.1453+10633G>T		intron_variant	Intron 6 of 9	ENST00000265997.5	NP_055727.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPEB3	ENST00000265997.5	c.1453+10633G>T		intron_variant	Intron 6 of 9	1	NM_014912.5	ENSP00000265997.4
CPEB3	ENST00000412050.8	c.1411+10633G>T		intron_variant	Intron 6 of 9	1		ENSP00000398310.2
CPEB3	ENST00000614585.4	c.1453+10633G>T		intron_variant	Intron 6 of 9	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

African (AFR) AF: 0.137 AC: 5696 AN: 41428

American (AMR) AF: 0.365 AC: 5555 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1416 AN: 3472

East Asian (EAS) AF: 0.305 AC: 1574 AN: 5168

South Asian (SAS) AF: 0.133 AC: 643 AN: 4818

European-Finnish (FIN) AF: 0.265 AC: 2790 AN: 10532

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.338 AC: 22987 AN: 67910

Other (OTH) AF: 0.329 AC: 692 AN: 2106

Alfa AF: 0.296 Hom.: 4747

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
PhyloP100		0.058
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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