rs2252745

chr6-30611538-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
PPP1R10	NM_002714.4	c.-11-1583G>A		intron_variant		ENST00000376511.7
PPP1R10	NM_001376195.1	c.-11-1583G>A		intron_variant
PPP1R10	XM_011514722.2	c.-11-1583G>A		intron_variant
PPP1R10	NR_072994.2	n.542-1583G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP1R10	ENST00000376511.7	c.-11-1583G>A		intron_variant		1	NM_002714.4	P1
PPP1R10	ENST00000484449.1	n.597-1583G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.843

Gnomad4 EAS AF: 0.704

Gnomad4 SAS AF: 0.876

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.748

Alfa AF: 0.708 Hom.: 56439

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

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: rs2252745; hg19: chr6-30579315;