rs9262122

Positions:

• chr6-30606065-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002714.4(PPP1R10):​c.741-30A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 1,612,602 control chromosomes in the GnomAD database, including 18,548 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 0.12 (1390 hom., cov: 31)
  • Exomes 𝑓: 0.15 (17158 hom.)
• Consequence: PPP1R10 NM_002714.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

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=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPP1R10	NM_002714.4	c.741-30A>G		intron_variant		ENST00000376511.7
PPP1R10	NM_001376195.1	c.741-30A>G		intron_variant
PPP1R10	XM_011514722.2	c.741-30A>G		intron_variant
PPP1R10	NR_072994.2	n.1293-30A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP1R10	ENST00000376511.7	c.741-30A>G		intron_variant		1	NM_002714.4	P1
PPP1R10	ENST00000461593.5	n.377-30A>G		intron_variant, non_coding_transcript_variant		2
PPP1R10	ENST00000468181.1	n.107-30A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17909 AN: 151916 Hom.: 1389 Cov.: 31

Gnomad AFR AF: 0.0294

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0659

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.124

GnomAD3 exomes AF: 0.153 AC: 38512 AN: 251242 Hom.: 3412 AF XY: 0.157 AC XY: 21359 AN XY: 135782

Gnomad AFR exome AF: 0.0242

Gnomad AMR exome AF: 0.204

Gnomad ASJ exome AF: 0.118

Gnomad EAS exome AF: 0.0531

Gnomad SAS exome AF: 0.203

Gnomad FIN exome AF: 0.169

Gnomad NFE exome AF: 0.159

Gnomad OTH exome AF: 0.152

GnomAD4 exome AF: 0.148 AC: 216495 AN: 1460568 Hom.: 17158 Cov.: 34 AF XY: 0.151 AC XY: 109544 AN XY: 726692

Gnomad4 AFR exome AF: 0.0216

Gnomad4 AMR exome AF: 0.199

Gnomad4 ASJ exome AF: 0.123

Gnomad4 EAS exome AF: 0.0567

Gnomad4 SAS exome AF: 0.202

Gnomad4 FIN exome AF: 0.169

Gnomad4 NFE exome AF: 0.149

Gnomad4 OTH exome AF: 0.141

GnomAD4 genome AF: 0.118 AC: 17917 AN: 152034 Hom.: 1390 Cov.: 31 AF XY: 0.120 AC XY: 8903 AN XY: 74302

Gnomad4 AFR AF: 0.0294

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.0661

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.122

Alfa AF: 0.144 Hom.: 1313

Bravo AF: 0.114

Asia WGS AF: 0.119 AC: 414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.55
DANN	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs9262122; hg19: chr6-30573842; COSMIC: COSV64739130; COSMIC: COSV64739130;