4-15040478-CGA-AGG

Variant names:

• chr4-15040478-CGA-AGG
• NM_001177382.2:c.2191_2193delCGAinsAGG
• CPEB2 p.732

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001177382.2(CPEB2):​c.2191_2193delCGAinsAGG​(p.732) variant causes a synonymous change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CPEB2 NM_001177382.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.27
• Publications: 0 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: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001177382.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPEB2	NM_001177382.2	MANE Select	c.2191_2193delCGAinsAGG	p.732	synonymous	N/A	NP_001170853.1	Q7Z5Q1-9
	CPEB2	NM_001177381.2		c.2110_2112delCGAinsAGG	p.705	synonymous	N/A	NP_001170852.1	Q7Z5Q1-8
	CPEB2	NM_001177383.2		c.2101_2103delCGAinsAGG	p.702	synonymous	N/A	NP_001170854.1	A0A5K1VW71

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPEB2	ENST00000538197.7	TSL:5 MANE Select	c.2191_2193delCGAinsAGG	p.732	synonymous	N/A	ENSP00000443985.1	Q7Z5Q1-9
	CPEB2	ENST00000382395.8	TSL:1	c.2101_2103delCGAinsAGG	p.702	synonymous	N/A	ENSP00000371832.4	A0A5K1VW71
	CPEB2	ENST00000507071.6	TSL:1	c.2176+7267_2176+7269delCGAinsAGG		intron	N/A	ENSP00000424084.2	A0A5K1VW93

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr4-15042102;