rs767477847

Variant names:

• chr5-173890322-G-A
• rs767477847
• NM_030627.4:c.589G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-173890322-G-A
• chr5-173890322-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_030627.4(CPEB4):​c.589G>A​(p.Ala197Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CPEB4 NM_030627.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.08

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 Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.084376246).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPEB4	NM_030627.4	c.589G>A	p.Ala197Thr	missense_variant	Exon 1 of 10	ENST00000265085.10	NP_085130.2
CPEB4	NM_001308189.2	c.589G>A	p.Ala197Thr	missense_variant	Exon 1 of 9		NP_001295118.1
CPEB4	NM_001308191.2	c.589G>A	p.Ala197Thr	missense_variant	Exon 1 of 8		NP_001295120.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPEB4	ENST00000265085.10	c.589G>A	p.Ala197Thr	missense_variant	Exon 1 of 10	1	NM_030627.4	ENSP00000265085.5
CPEB4	ENST00000334035.9	c.589G>A	p.Ala197Thr	missense_variant	Exon 1 of 9	1		ENSP00000334533.5
CPEB4	ENST00000520867.5	c.589G>A	p.Ala197Thr	missense_variant	Exon 1 of 8	1		ENSP00000429092.1
CPEB4	ENST00000519835.5	c.589G>A	p.Ala197Thr	missense_variant	Exon 1 of 7	1		ENSP00000429048.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ExAC AF: 0.00000824 AC: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.068
BayesDel_addAF	Benign	-0.25	T
BayesDel_noAF	Benign	-0.59
CADD	Benign	23
DANN	Benign	0.91
DEOGEN2	Benign	0.016	T;.;.;T
Eigen	Benign	-0.50
Eigen_PC	Benign	-0.28
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Benign	0.81	T;T;T;T
M_CAP	Benign	0.0051	T
MetaRNN	Benign	0.084	T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.34	N;.;N;.
PrimateAI	Uncertain	0.56	T
PROVEAN	Benign	-0.11	N;N;N;N
REVEL	Benign	0.062
Sift	Benign	0.43	T;T;T;T
Sift4G	Benign	0.88	T;T;T;T
Polyphen		0.0	B;B;B;B
Vest4		0.044
MutPred		0.18		Gain of glycosylation at A197 (P = 0.0134);Gain of glycosylation at A197 (P = 0.0134);Gain of glycosylation at A197 (P = 0.0134);Gain of glycosylation at A197 (P = 0.0134);
MVP		0.30
MPC		0.40
ClinPred		0.53	D
GERP RS		5.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.045
gMVP		0.27

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: rs767477847; hg19: chr5-173317325;