NM_002714.4:c.-11-1583G>A

Variant names:

• chr6-30611538-C-T
• rs2252745
• NM_002714.4:c.-11-1583G>A

Variant summary

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

The NM_002714.4(PPP1R10):​c.-11-1583G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.741 in 152,092 control chromosomes in the GnomAD database, including 42,147 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 0.74 (42147 hom., cov: 32)
• Consequence: PPP1R10 NM_002714.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.569
• Publications: 24 publications found

Genes affected

PPP1R10 (HGNC:9284): (protein phosphatase 1 regulatory subunit 10) This gene encodes a protein phosphatase 1 binding protein. The encoded protein plays a role in many cellular processes including cell cycle progression, DNA repair and apoptosis by regulating the activity of protein phosphatase 1. This gene lies within the major histocompatibility complex class I region on chromosome 6, and alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jul 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP1R10	NM_002714.4	c.-11-1583G>A		intron_variant	Intron 2 of 19	ENST00000376511.7	NP_002705.2
PPP1R10	NM_001376195.1	c.-11-1583G>A		intron_variant	Intron 2 of 19		NP_001363124.1
PPP1R10	NR_072994.2	n.542-1583G>A		intron_variant	Intron 2 of 19
PPP1R10	XM_011514722.2	c.-11-1583G>A		intron_variant	Intron 3 of 20		XP_011513024.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1R10	ENST00000376511.7	c.-11-1583G>A		intron_variant	Intron 2 of 19	1	NM_002714.4	ENSP00000365694.2
PPP1R10	ENST00000484449.1	n.597-1583G>A		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112535 AN: 151974 Hom.: 42104 Cov.: 32

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.822

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.741 AC: 112634 AN: 152092 Hom.: 42147 Cov.: 32 AF XY: 0.738 AC XY: 54891 AN XY: 74344

African (AFR) AF: 0.844 AC: 35030 AN: 41500

American (AMR) AF: 0.669 AC: 10212 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2928 AN: 3472

East Asian (EAS) AF: 0.704 AC: 3643 AN: 5176

South Asian (SAS) AF: 0.876 AC: 4229 AN: 4826

European-Finnish (FIN) AF: 0.685 AC: 7226 AN: 10554

Middle Eastern (MID) AF: 0.815 AC: 238 AN: 292

European-Non Finnish (NFE) AF: 0.689 AC: 46861 AN: 67976

Other (OTH) AF: 0.748 AC: 1580 AN: 2112

Alfa AF: 0.711 Hom.: 142054

Bravo AF: 0.744

Asia WGS AF: 0.811 AC: 2820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	0.27
DANN	Benign	0.86
PhyloP100		-0.57
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: rs2252745; hg19: chr6-30579315;