rs2303846

Variant names:

• chr15-82544529-G-A
• rs2303846
• NM_001365242.1:c.*63C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001365242.1(CPEB1):​c.*63C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0932 in 1,267,352 control chromosomes in the GnomAD database, including 7,247 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 0.14 (1884 hom., cov: 32)
  • Exomes 𝑓: 0.088 (5363 hom.)
• Consequence: CPEB1 NM_001365242.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 2 publications found

Genes affected

CPEB1 (HGNC:21744): (cytoplasmic polyadenylation element binding protein 1) This gene encodes a member of the cytoplasmic polyadenylation element binding protein family. This highly conserved protein binds to a specific RNA sequence, called the cytoplasmic polyadenylation element, found in the 3' untranslated region of some mRNAs. The encoded protein functions in both the cytoplasm and the nucleus. It is involved in the regulation of mRNA translation, as well as processing of the 3' untranslated region, and may play a role in cell proliferation and tumorigenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

ENSG00000260836 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPEB1	NM_001365242.1	c.*63C>T		3_prime_UTR_variant	Exon 13 of 13	ENST00000684509.1	NP_001352171.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPEB1	ENST00000684509.1	c.*63C>T		3_prime_UTR_variant	Exon 13 of 13		NM_001365242.1	ENSP00000507835.1
ENSG00000260836	ENST00000562833.2	c.1350+1912C>T		intron_variant	Intron 9 of 12	3		ENSP00000454786.2

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20544 AN: 152134 Hom.: 1882 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.0549

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.0927

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.0625

Gnomad FIN AF: 0.0654

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0753

Gnomad OTH AF: 0.131

GnomAD4 exome AF: 0.0875 AC: 97591 AN: 1115100 Hom.: 5363 Cov.: 14 AF XY: 0.0853 AC XY: 48029 AN XY: 563094

African (AFR) AF: 0.240 AC: 6443 AN: 26876

American (AMR) AF: 0.182 AC: 6789 AN: 37300

Ashkenazi Jewish (ASJ) AF: 0.0821 AC: 1770 AN: 21564

East Asian (EAS) AF: 0.215 AC: 7947 AN: 37002

South Asian (SAS) AF: 0.0615 AC: 4488 AN: 73028

European-Finnish (FIN) AF: 0.0664 AC: 3317 AN: 49928

Middle Eastern (MID) AF: 0.107 AC: 366 AN: 3432

European-Non Finnish (NFE) AF: 0.0755 AC: 61741 AN: 817666

Other (OTH) AF: 0.0979 AC: 4730 AN: 48304

GnomAD4 genome AF: 0.135 AC: 20570 AN: 152252 Hom.: 1884 Cov.: 32 AF XY: 0.135 AC XY: 10060 AN XY: 74442

African (AFR) AF: 0.237 AC: 9856 AN: 41538

American (AMR) AF: 0.179 AC: 2743 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0927 AC: 322 AN: 3472

East Asian (EAS) AF: 0.227 AC: 1175 AN: 5176

South Asian (SAS) AF: 0.0622 AC: 300 AN: 4826

European-Finnish (FIN) AF: 0.0654 AC: 693 AN: 10604

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0754 AC: 5126 AN: 68020

Other (OTH) AF: 0.130 AC: 275 AN: 2116

Alfa AF: 0.115 Hom.: 116

Bravo AF: 0.146

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	10
DANN	Benign	0.84
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs2303846; hg19: chr15-83213279;