rs17107517

chr10-92273716-T-C

Variant summary

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

The NM_014912.5(CPEB3):c.-12+17210A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,038 control chromosomes in the GnomAD database, including 10,516 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 0.35 (10516 hom., cov: 32)
• Consequence: CPEB3 NM_014912.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500

Genes affected

CPEB3 (HGNC:21746): (cytoplasmic polyadenylation element binding protein 3) Enables mRNA 3'-UTR binding activity and translation factor activity, RNA binding. Involved in cellular response to amino acid stimulus; negative regulation of transcription by RNA polymerase II; and positive regulation of mRNA catabolic process. Located in several cellular components, including cytosol; midbody; and nucleoplasm. Part of CCR4-NOT complex. [provided by Alliance of Genome Resources, Apr 2022]

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 (AFR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPEB3	NM_014912.5	c.-12+17210A>G		intron_variant		ENST00000265997.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPEB3	ENST00000265997.5	c.-12+17210A>G		intron_variant		1	NM_014912.5

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53309 AN: 151920 Hom.: 10500 Cov.: 32

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.351 AC: 53370 AN: 152038 Hom.: 10516 Cov.: 32 AF XY: 0.342 AC XY: 25389 AN XY: 74324

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.362

Alfa AF: 0.334 Hom.: 1537

Bravo AF: 0.365

Asia WGS AF: 0.154 AC: 535 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	4.0
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17107517; hg19: chr10-94033473;