rs2604578

chr4-15044272-A-G

Variant summary

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

The NM_001177382.2(CPEB2):c.2200+3785A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 151,968 control chromosomes in the GnomAD database, including 21,646 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 0.53 (21646 hom., cov: 32)
• Consequence: CPEB2 NM_001177382.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPEB2	NM_001177382.2	c.2200+3785A>G		intron_variant		ENST00000538197.7
C1QTNF7-AS1	NR_125911.1	n.155-26391T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPEB2	ENST00000538197.7	c.2200+3785A>G		intron_variant		5	NM_001177382.2	P3
C1QTNF7-AS1	ENST00000502344.5	n.155-26391T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80264 AN: 151850 Hom.: 21647 Cov.: 32

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.528 AC: 80280 AN: 151968 Hom.: 21646 Cov.: 32 AF XY: 0.526 AC XY: 39049 AN XY: 74272

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.523

Alfa AF: 0.567 Hom.: 44310

Bravo AF: 0.517

Asia WGS AF: 0.396 AC: 1376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.14
Dann	Benign	0.56

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: rs2604578; hg19: chr4-15045896;