rs701846

Variant names:

• chr10-92111309-G-A
• rs701846
• NM_014912.5:c.1454-115C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-92111309-G-A
• chr10-92111309-G-C
• chr10-92111309-G-T

Variant summary

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

The NM_014912.5(CPEB3):​c.1454-115C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 744,904 control chromosomes in the GnomAD database, including 141,741 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 0.68 (36746 hom., cov: 34)
  • Exomes 𝑓: 0.59 (104995 hom.)
• Consequence: CPEB3 NM_014912.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 9 publications found

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]

CPEB3 Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPEB3	NM_014912.5	c.1454-115C>T		intron_variant	Intron 6 of 9	ENST00000265997.5	NP_055727.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPEB3	ENST00000265997.5	c.1454-115C>T		intron_variant	Intron 6 of 9	1	NM_014912.5	ENSP00000265997.4
CPEB3	ENST00000412050.8	c.1412-115C>T		intron_variant	Intron 6 of 9	1		ENSP00000398310.2
CPEB3	ENST00000614585.4	c.1454-115C>T		intron_variant	Intron 6 of 9	5		ENSP00000482128.1

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103337 AN: 152122 Hom.: 36709 Cov.: 34

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.708

GnomAD4 exome AF: 0.589 AC: 348794 AN: 592664 Hom.: 104995 AF XY: 0.581 AC XY: 184128 AN XY: 316896

African (AFR) AF: 0.889 AC: 14256 AN: 16044

American (AMR) AF: 0.708 AC: 24429 AN: 34482

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 11513 AN: 17578

East Asian (EAS) AF: 0.504 AC: 17893 AN: 35500

South Asian (SAS) AF: 0.443 AC: 26011 AN: 58720

European-Finnish (FIN) AF: 0.488 AC: 23295 AN: 47760

Middle Eastern (MID) AF: 0.675 AC: 1531 AN: 2268

European-Non Finnish (NFE) AF: 0.603 AC: 210674 AN: 349122

Other (OTH) AF: 0.615 AC: 19192 AN: 31190

GnomAD4 genome AF: 0.679 AC: 103433 AN: 152240 Hom.: 36746 Cov.: 34 AF XY: 0.668 AC XY: 49734 AN XY: 74424

African (AFR) AF: 0.886 AC: 36805 AN: 41546

American (AMR) AF: 0.715 AC: 10941 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2333 AN: 3472

East Asian (EAS) AF: 0.528 AC: 2735 AN: 5178

South Asian (SAS) AF: 0.434 AC: 2096 AN: 4828

European-Finnish (FIN) AF: 0.482 AC: 5111 AN: 10600

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41268 AN: 68006

Other (OTH) AF: 0.709 AC: 1495 AN: 2110

Alfa AF: 0.627 Hom.: 21123

Bravo AF: 0.714

Asia WGS AF: 0.499 AC: 1739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.81
DANN	Benign	0.40
PhyloP100		-1.6
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: rs701846; hg19: chr10-93871066;