rs783540

Variant names:

• chr15-82585958-A-G
• rs783540
• NM_001365242.1:c.272-14426T>C

Your query was ambiguous. Multiple possible variants found:

• chr15-82585958-A-G
• chr15-82585958-A-T

Variant summary

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

The NM_001365242.1(CPEB1):​c.272-14426T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 151,496 control chromosomes in the GnomAD database, including 12,423 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 0.40 (12423 hom., cov: 30)
• Consequence: CPEB1 NM_001365242.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.667

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPEB1	NM_001365242.1	c.272-14426T>C		intron_variant	Intron 3 of 12	ENST00000684509.1	NP_001352171.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPEB1	ENST00000684509.1	c.272-14426T>C		intron_variant	Intron 3 of 12		NM_001365242.1	ENSP00000507835.1

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61274 AN: 151378 Hom.: 12421 Cov.: 30

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.405 AC: 61292 AN: 151496 Hom.: 12423 Cov.: 30 AF XY: 0.408 AC XY: 30218 AN XY: 74038

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.410

Alfa AF: 0.386 Hom.: 13799

Bravo AF: 0.395

Asia WGS AF: 0.431 AC: 1500 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.4
DANN	Benign	0.69

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: rs783540; hg19: chr15-83254708;