rs7071217

Variant names:

• chr10-92179405-T-C
• rs7071217
• NM_014912.5:c.1222+1558A>G

Variant summary

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

The NM_014912.5(CPEB3):​c.1222+1558A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,218 control chromosomes in the GnomAD database, including 1,351 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 0.12 (1351 hom., cov: 32)
• Consequence: CPEB3 NM_014912.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.487
• Publications: 3 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=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014912.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPEB3	NM_014912.5	MANE Select	c.1222+1558A>G		intron	N/A	NP_055727.3
	CPEB3	NM_001178137.2		c.1153+1558A>G		intron	N/A	NP_001171608.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPEB3	ENST00000265997.5	TSL:1 MANE Select	c.1222+1558A>G		intron	N/A	ENSP00000265997.4
	CPEB3	ENST00000412050.8	TSL:1	c.1153+1558A>G		intron	N/A	ENSP00000398310.2
	CPEB3	ENST00000614585.4	TSL:5	c.1222+1558A>G		intron	N/A	ENSP00000482128.1

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18561 AN: 152100 Hom.: 1352 Cov.: 32

Gnomad AFR AF: 0.0624

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0112

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.122 AC: 18549 AN: 152218 Hom.: 1351 Cov.: 32 AF XY: 0.120 AC XY: 8964 AN XY: 74416

African (AFR) AF: 0.0622 AC: 2586 AN: 41546

American (AMR) AF: 0.137 AC: 2097 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 654 AN: 3470

East Asian (EAS) AF: 0.0112 AC: 58 AN: 5186

South Asian (SAS) AF: 0.115 AC: 555 AN: 4824

European-Finnish (FIN) AF: 0.129 AC: 1362 AN: 10586

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.159 AC: 10785 AN: 67996

Other (OTH) AF: 0.150 AC: 316 AN: 2112

Alfa AF: 0.129 Hom.: 310

Bravo AF: 0.120

Asia WGS AF: 0.0750 AC: 261 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	15
DANN	Benign	0.89
PhyloP100		0.49
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: rs7071217; hg19: chr10-93939162;