rs1106693

Positions:

• chr5-173925760-G-A
• chr5-173925760-G-C

Variant summary

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

The NM_030627.4(CPEB4):​c.1208-6690G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.941 in 152,282 control chromosomes in the GnomAD database, including 67,474 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 0.94 (67474 hom., cov: 32)
• Consequence: CPEB4 NM_030627.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.725

Genes affected

CPEB4 (HGNC:21747): (cytoplasmic polyadenylation element binding protein 4) Enables RNA binding activity. Predicted to be involved in several processes, including cellular response to glucose starvation; negative regulation of cytoplasmic translation; and response to ischemia. Located in cytoplasm and nucleus. Biomarker of liver cirrhosis; portal hypertension; and primary biliary cholangitis. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPEB4	NM_030627.4	c.1208-6690G>A		intron_variant		ENST00000265085.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPEB4	ENST00000265085.10	c.1208-6690G>A		intron_variant		1	NM_030627.4

Frequencies

GnomAD3 genomes AF: 0.941 AC: 143184 AN: 152164 Hom.: 67423 Cov.: 32

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.954

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.974

Gnomad FIN AF: 0.974

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.955

Gnomad OTH AF: 0.943

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

GnomAD4 genome AF: 0.941 AC: 143292 AN: 152282 Hom.: 67474 Cov.: 32 AF XY: 0.942 AC XY: 70170 AN XY: 74462

Gnomad4 AFR AF: 0.892

Gnomad4 AMR AF: 0.954

Gnomad4 ASJ AF: 0.967

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.974

Gnomad4 FIN AF: 0.974

Gnomad4 NFE AF: 0.955

Gnomad4 OTH AF: 0.943

Alfa AF: 0.950 Hom.: 65393

Bravo AF: 0.937

Asia WGS AF: 0.982 AC: 3414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.49

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: rs1106693; hg19: chr5-173352763;