rs7705502

Variant names:

• chr5-173893812-G-A
• rs7705502
• NM_030627.4:c.1125+2954G>A

Variant summary

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

The NM_030627.4(CPEB4):​c.1125+2954G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,046 control chromosomes in the GnomAD database, including 4,967 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 0.22 (4967 hom., cov: 31)
• Consequence: CPEB4 NM_030627.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168
• Publications: 39 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPEB4	NM_030627.4	c.1125+2954G>A		intron_variant	Intron 1 of 9	ENST00000265085.10	NP_085130.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPEB4	ENST00000265085.10	c.1125+2954G>A		intron_variant	Intron 1 of 9	1	NM_030627.4	ENSP00000265085.5

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33796 AN: 151928 Hom.: 4969 Cov.: 31

Gnomad AFR AF: 0.0671

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0812

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.222 AC: 33784 AN: 152046 Hom.: 4967 Cov.: 31 AF XY: 0.225 AC XY: 16747 AN XY: 74314

African (AFR) AF: 0.0669 AC: 2775 AN: 41484

American (AMR) AF: 0.185 AC: 2832 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1029 AN: 3470

East Asian (EAS) AF: 0.0808 AC: 418 AN: 5174

South Asian (SAS) AF: 0.107 AC: 517 AN: 4822

European-Finnish (FIN) AF: 0.455 AC: 4799 AN: 10538

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20753 AN: 67966

Other (OTH) AF: 0.188 AC: 398 AN: 2114

Alfa AF: 0.284 Hom.: 10758

Bravo AF: 0.196

Asia WGS AF: 0.0870 AC: 306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.35
PhyloP100		0.17
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: rs7705502; hg19: chr5-173320815;