chr4-15051323-T-G

Variant names:

• chr4-15051323-T-G
• rs10516283
• NM_001177382.2:c.2201-1091T>G

Variant summary

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

The NM_001177382.2(CPEB2):​c.2201-1091T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 152,000 control chromosomes in the GnomAD database, including 18,557 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 0.48 (18557 hom., cov: 32)
• Consequence: CPEB2 NM_001177382.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.223
• Publications: 2 publications found

Genes affected

CPEB2 (HGNC:21745): (cytoplasmic polyadenylation element binding protein 2) The protein encoded by this gene is highly similar to cytoplasmic polyadenylation element binding protein (CPEB), an mRNA-binding protein that regulates cytoplasmic polyadenylation of mRNA as a trans factor in oogenesis and spermatogenesis. Studies of the similar gene in mice suggested a possible role of this protein in transcriptionally inactive haploid spermatids. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jul 2008]

C1QTNF7-AS1 (HGNC:40683): (C1QTNF7 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPEB2	NM_001177382.2	c.2201-1091T>G		intron_variant	Intron 6 of 11	ENST00000538197.7	NP_001170853.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPEB2	ENST00000538197.7	c.2201-1091T>G		intron_variant	Intron 6 of 11	5	NM_001177382.2	ENSP00000443985.1

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73246 AN: 151882 Hom.: 18531 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.482 AC: 73298 AN: 152000 Hom.: 18557 Cov.: 32 AF XY: 0.486 AC XY: 36126 AN XY: 74304

African (AFR) AF: 0.351 AC: 14565 AN: 41460

American (AMR) AF: 0.575 AC: 8784 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1399 AN: 3462

East Asian (EAS) AF: 0.754 AC: 3892 AN: 5164

South Asian (SAS) AF: 0.284 AC: 1368 AN: 4816

European-Finnish (FIN) AF: 0.606 AC: 6403 AN: 10566

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35360 AN: 67950

Other (OTH) AF: 0.468 AC: 985 AN: 2106

Alfa AF: 0.490 Hom.: 7724

Bravo AF: 0.482

Asia WGS AF: 0.480 AC: 1670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.9
DANN	Benign	0.34
PhyloP100		0.22
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: rs10516283; hg19: chr4-15052947;