5-173921153-G-A

Variant names:

• chr5-173921153-G-A
• rs10516107
• NM_030627.4:c.1207+10549G>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.1207+10549G>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 152,036 control chromosomes in the GnomAD database, including 4,964 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 (4964 hom., cov: 32)
• Consequence: CPEB4 NM_030627.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 20 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=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030627.4. 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
	CPEB4	NM_030627.4	MANE Select	c.1207+10549G>A		intron	N/A	NP_085130.2
	CPEB4	NM_001308189.2		c.1207+10549G>A		intron	N/A	NP_001295118.1
	CPEB4	NM_001308191.2		c.1207+10549G>A		intron	N/A	NP_001295120.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPEB4	ENST00000265085.10	TSL:1 MANE Select	c.1207+10549G>A		intron	N/A	ENSP00000265085.5
	CPEB4	ENST00000334035.9	TSL:1	c.1207+10549G>A		intron	N/A	ENSP00000334533.5
	CPEB4	ENST00000520867.5	TSL:1	c.1207+10549G>A		intron	N/A	ENSP00000429092.1

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33769 AN: 151918 Hom.: 4966 Cov.: 32

Gnomad AFR AF: 0.0669

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.0802

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.222 AC: 33757 AN: 152036 Hom.: 4964 Cov.: 32 AF XY: 0.225 AC XY: 16719 AN XY: 74290

African (AFR) AF: 0.0667 AC: 2768 AN: 41494

American (AMR) AF: 0.185 AC: 2833 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1028 AN: 3470

East Asian (EAS) AF: 0.0799 AC: 413 AN: 5172

South Asian (SAS) AF: 0.107 AC: 517 AN: 4820

European-Finnish (FIN) AF: 0.455 AC: 4795 AN: 10540

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

European-Non Finnish (NFE) AF: 0.305 AC: 20742 AN: 67944

Other (OTH) AF: 0.189 AC: 398 AN: 2110

Alfa AF: 0.259 Hom.: 785

Bravo AF: 0.197

Asia WGS AF: 0.0870 AC: 305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	14
DANN	Benign	0.70
PhyloP100		0.027
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: rs10516107; hg19: chr5-173348156;