chr14-23297382-G-T

Variant names:

• chr14-23297382-G-T
• rs1884056
• NM_001276318.2:c.*1922C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001276318.2(PPP1R3E):​c.*1922C>A variant causes a 3 prime UTR 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PPP1R3E NM_001276318.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 14 publications found

Genes affected

PPP1R3E (HGNC:14943): (protein phosphatase 1 regulatory subunit 3E) Predicted to enable [phosphorylase] phosphatase activity; glycogen binding activity; and protein phosphatase 1 binding activity. Predicted to be involved in positive regulation of glycogen biosynthetic process. Predicted to be located in glycogen granule. Predicted to be part of protein phosphatase type 1 complex. [provided by Alliance of Genome Resources, Apr 2022]

HOMEZ (HGNC:20164): (homeobox and leucine zipper encoding) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in cytosol; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001276318.2. 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
	PPP1R3E	NM_001276318.2	MANE Select	c.*1922C>A		3_prime_UTR	Exon 5 of 5	NP_001263247.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R3E	ENST00000452015.9	TSL:2 MANE Select	c.*1922C>A		3_prime_UTR	Exon 5 of 5	ENSP00000408288.3
	PPP1R3E	ENST00000558058.5	TSL:3	c.*1727C>A		3_prime_UTR	Exon 4 of 4	ENSP00000453175.1
	PPP1R3E	ENST00000559314.5	TSL:2	c.*1242C>A		3_prime_UTR	Exon 5 of 5	ENSP00000454106.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.62
PhyloP100		0.25

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: rs1884056; hg19: chr14-23766591;